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(-) Description

Title :  CRYSTAL STRUCTURE OF CAS9-SGRNA-DNA COMPLEX SOLVED BY NATIVE SAD PHASING
 
Authors :  V. Olieric, T. Weinert, A. Finke, C. Anders, M. Jinek, M. Wang
Date :  07 Dec 15  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Hydrolase-Dna Complex, Crispr, Cas9, Genome Editing, Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Olieric, T. Weinert, A. D. Finke, C. Anders, D. Li, N. Olieric, C. N. Borca, M. O. Steinmetz, M. Caffrey, M. Jinek, M. Wang
Data-Collection Strategy For Challenging Native Sad Phasing
Acta Crystallogr. , Sect. D V. 72 421 2016
PubMed-ID: 26960129  |  Reference-DOI: 10.1107/S2059798315024110

(-) Compounds

Molecule 1 - SGRNA
    Chains: A
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
    Chains: B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEC-K-MBP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2
    Expression System Vector Type: PLASMID
    Gene: CAS9, CSN1, SPY_1046
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    Synonym: SPYCAS9
 
Molecule 3 - TARGET DNA STRAND PROXIMAL FRAGMENT
    Chains: C
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - NON-TARGET DNA STRAND
    Chains: D
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 5 - TARGET DNA STRAND DISTAL FRAGMENT
    Chains: E
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1K13Ligand/IonPOTASSIUM ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREA A:65 , U A:66 , HOH A:3252 , HOH A:3278 , HOH A:3279 , THR B:1102BINDING SITE FOR RESIDUE K A2083
02AC2SOFTWAREG A:21 , HOH A:3006 , HOH A:3156 , HOH A:3158 , HOH A:3299BINDING SITE FOR RESIDUE K A2084
03AC3SOFTWAREA A:68 , HOH A:3280 , HOH A:3283 , GLN B:1350 , HOH B:3588BINDING SITE FOR RESIDUE K B2365
04AC4SOFTWAREGLU B:584 , ARG B:586 , ASN B:588 , HOH B:3356 , HOH B:3357 , HOH E:3039BINDING SITE FOR RESIDUE K B2366
05AC5SOFTWAREHOH A:3102 , HOH A:3104 , HOH A:3112 , HOH A:3299 , HOH A:3300 , HOH A:3301BINDING SITE FOR RESIDUE MG A1083
06AC6SOFTWAREU A:50 , HOH A:3183 , HOH A:3184 , HOH A:3185 , HOH A:3187 , HOH A:3209BINDING SITE FOR RESIDUE MG A1084
07AC7SOFTWARELEU B:623 , THR B:624 , PHE B:626 , TYR B:656 , HOH B:3386BINDING SITE FOR RESIDUE K B2367
08AC8SOFTWAREHOH A:3107 , GLY B:361 , TYR B:362 , GLY B:365 , ALA B:367BINDING SITE FOR RESIDUE K B2368
09AC9SOFTWAREILE B:226 , LEU B:229 , GLU B:232 , HOH B:3021 , HOH B:3022 , HOH B:3174BINDING SITE FOR RESIDUE K B2369
10BC1SOFTWAREGLU B:108 , LYS B:111 , HOH B:3108 , HOH B:3109 , HOH B:3111BINDING SITE FOR RESIDUE K B2370
11BC2SOFTWAREASP B:576 , SER B:577 , ALA B:640 , PHE B:643 , HOH B:3396 , HOH B:3399 , HOH B:3401BINDING SITE FOR RESIDUE K B2371
12BC3SOFTWAREU A:12 , G A:13 , HOH A:3055 , HOH A:3060 , HOH A:3061BINDING SITE FOR RESIDUE K A1085
13BC4SOFTWAREHOH A:3254 , HOH A:3255 , HOH A:3263 , GLU B:57 , HOH B:3003 , HOH B:3053 , HOH B:3593BINDING SITE FOR RESIDUE K B2372
14BC5SOFTWAREU A:22 , HOH A:3109 , HOH A:3114 , ASP B:364 , GLY B:365BINDING SITE FOR RESIDUE K B2373
15BC6SOFTWAREDT D:5 , HOH D:3002 , HOH D:3003BINDING SITE FOR RESIDUE K D1013

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FQ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FQ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FQ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FQ5)

(-) Exons   (0, 0)

(no "Exon" information available for 5FQ5)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:DNA/RNA  Length:83
                                                                                                                    
                5fq5 A    0 GAUAACUCAAUUUGUAAAAAAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGA   82
                                     9        19        29        39        49        59        69        79   


Chain B from PDB  Type:PROTEIN  Length:1318
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee.......eeeeeeee.....eeeee.eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh............hhhhhhh...hhhhhhhhhhhh.......hhhhhhhhhhhh......................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhh..eee.......ee.hhhhhhhhhhhh.......hhhhhhhhh..........ee..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh........hhhhhhhh......hhhhhhhh...hhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhh...........hhhhhhhheeee..........hhh.eeee.hhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhh.............eeee.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhhh.hhhhh.......eee......eeee..hhhhhhhhhhhh...eeee..............................hhhhhh......eeeeeeeeeeeee....eeeeeeeeeeee..hhhhhhhhhhhhhhhhhee..hhhhheee....eee.hhh.eeee.....eee......hhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhh..........eee..eee.......hhhhhh.eeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fq5 B    4 KYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMAREKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDGKATAKYFFYSNIMNFFKTEIKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQ 1364
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173 ||    186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706      |720       730       740       750       760     ||778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008   || 1035      1045    ||1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243|     1256      1266      1276      1286      1296      1306      1316      1326      1336      1346      1356        
                                                                                                                                                                                                     175|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   713|                                             766|                                                                                                                                                                                                                                         1012|                1050|                                                                                                                                                                                    1243|                                                                                                                     
                                                                                                                                                                                                      179                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    718                                              775                                                                                                                                                                                                                                          1030                 1059                                                                                                                                                                                     1247                                                                                                                     


Chain C from PDB  Type:DNA  Length:9
                                          
                5fq5 C    1 CAATACCAC    9


Chain D from PDB  Type:DNA  Length:10
                                           
                5fq5 D    3 TGTGGTATTG   12
                                    12


Chain E from PDB  Type:DNA  Length:17
                                                  
                5fq5 E   12 TTTACAAATTGAGTTAT   28
                                    21
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5FQ5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FQ5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FQ5)

(-) Gene Ontology  (12, 12)

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        CAS9_STRP1 | Q99ZW2: 4cmp 4cmq 4oo8 4un3 4un4 4un5 4zt0 4zt9 5b2r 5b2s 5b2t 5f9r 5fw1 5fw2 5fw3 5vw1 5xbl

(-) Related Entries Specified in the PDB File

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