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(-) Description

Title :  CRYSTAL STRUCTURE OF CAS9 BOUND TO PAM-CONTAINING DNA TARGET WITH MISMATCHES AT POSITIONS 1-2
 
Authors :  C. Anders, O. Niewoehner, A. Duerst, M. Jinek
Date :  25 May 14  (Deposition) - 23 Jul 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Hydrolase-Dna-Rna Complex, Genome Editing, Rnp, Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Anders, O. Niewoehner, A. Duerst, M. Jinek
Structural Basis Of Pam-Dependent Target Dna Recognition By The Cas9 Endonuclease
Nature V. 513 569 2014
PubMed-ID: 25079318  |  Reference-DOI: 10.1038/NATURE13579

(-) 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: ROSETTA 2
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    Strain: M1
 
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  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1MG8Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:3067 , HOH A:3069 , HOH A:3070 , HOH A:3204BINDING SITE FOR RESIDUE MG A1082
2AC2SOFTWAREU A:50 , HOH A:3121 , HOH A:3122 , HOH A:3124 , HOH A:3138BINDING SITE FOR RESIDUE MG A1083
3AC3SOFTWAREA A:65 , U A:66 , HOH A:3171 , HOH A:3189 , THR B:1102BINDING SITE FOR RESIDUE MG A1084
4AC4SOFTWARELEU B:623 , THR B:624 , PHE B:626 , TYR B:656 , HOH B:3245BINDING SITE FOR RESIDUE MG B2365
5AC5SOFTWAREA A:68 , HOH A:3190 , HOH A:3192 , GLN B:1350 , HOH B:3351BINDING SITE FOR RESIDUE MG B2366
6AC6SOFTWAREILE B:226 , LEU B:229 , GLU B:232 , HOH B:3112BINDING SITE FOR RESIDUE MG B2367
7AC7SOFTWAREGLU B:584 , ARG B:586 , ASN B:588BINDING SITE FOR RESIDUE MG B2368
8AC8SOFTWAREG A:21 , HOH A:3066 , HOH A:3067 , HOH A:3102BINDING SITE FOR RESIDUE MG A1085

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UN4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4UN4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UN4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UN4)

(-) Exons   (0, 0)

(no "Exon" information available for 4UN4)

(-) 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:82
                                                                                                                   
                4un4 A    0 GAUAACUCAAUUUGUAAAAAAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG   81
                                     9        19        29        39        49        59        69        79  


Chain B from PDB  Type:PROTEIN  Length:1310
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee.......eeeeeeee.....eeeee.eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.................hhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhh.......hhhhhhhhhhhh......................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhh..eee.......ee.hhhhhhhhhhhh.......hhhhhhhhh..........ee..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhh........hhhhhhh........hhhhhhhh......hhhhhhh....hhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhh...........hhhhhhhheeee..........hhh.eeee.hhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhh.ee.....ee...eeee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhhh.hhhhh.......eee......eeee..hhhhhhhhhhh....eeee.......................ee.....hhhhhhee....eeeeeeeeeeeee....eeeeeeeeeeee..hhhhhhhhhhhhhhhhh....hhhhheee....eee.....eeee.....eee......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh..........ee....ee........hhhhh.eeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4un4 B    4 KYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDGKATAKYFFYSNIMNFFKTEIKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQ 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     ||721       731       741       751       761   ||  780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010 ||   1037      1047  ||  1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235     |1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364
                                                                                                                                                                                                      176|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 712|                                            765|                                                                                                                                                                                                                                         1012|                1050|                                                                                                                                                                                  1241|                                                                                                                 
                                                                                                                                                                                                       180                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  718                                             775                                                                                                                                                                                                                                          1030                 1059                                                                                                                                                                                   1251                                                                                                                 


Chain C from PDB  Type:DNA  Length:11
                                            
                4un4 C    1 CAATACCACAT   11
                                    10 


Chain D from PDB  Type:DNA  Length:10
                                           
                4un4 D    3 TGTGGTATTG   12
                                    12


Chain E from PDB  Type:DNA  Length:17
                                                  
                4un4 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 4UN4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UN4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UN4)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  CAS9_STRP1 | Q99ZW2
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CAS9_STRP1 | Q99ZW2: 4cmp 4cmq 4oo8 4un3 4un5 4zt0 4zt9 5b2r 5b2s 5b2t 5f9r 5fq5 5fw1 5fw2 5fw3 5vw1 5xbl

(-) Related Entries Specified in the PDB File

4un3 CRYSTAL STRUCTURE OF CAS9 BOUND TO PAM-CONTAINING DNA TARGET
4un5 CRYSTAL STRUCTURE OF CAS9 BOUND TO PAM-CONTAINING DNA TARGET CONTAINING MISMATCHES AT POSITIONS 1-3