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(-) Description

Title :  CRYSTAL STRUCTURE OF CAS9 BOUND TO PAM-CONTAINING DNA TARGET
 
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 :  2.59
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase-Dna-Rna Complex, Crispr, 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 - 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
    Synonym: CAS9
 
Molecule 2 - SGRNA
    Chains: A
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - TARGET DNA STRAND
    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

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

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:2043 , HOH A:2045BINDING SITE FOR RESIDUE MG A1085
2AC2SOFTWAREU A:50 , HOH A:2083 , HOH A:2084 , HOH A:2085 , HOH A:2086 , HOH A:2101BINDING SITE FOR RESIDUE MG A1082
3AC3SOFTWAREA A:65 , U A:66 , HOH A:2137 , THR B:1102BINDING SITE FOR RESIDUE MG A1083
4AC4SOFTWAREASP B:10 , GLU B:762 , ASP B:986BINDING SITE FOR RESIDUE MG B2365
5AC5SOFTWARELEU B:623 , THR B:624 , PHE B:626 , TYR B:656 , HOH B:2139BINDING SITE FOR RESIDUE MG B2366
6AC6SOFTWAREA A:68 , HOH A:2138 , HOH A:2140 , GLN B:1350 , SER B:1351 , HOH B:2184 , HOH B:2242BINDING SITE FOR RESIDUE MG B2367
7AC7SOFTWAREGLU B:584 , ARG B:586 , ASN B:588 , HOH B:2128BINDING SITE FOR RESIDUE MG B2368
8AC8SOFTWAREG A:21 , HOH A:2041 , HOH A:2043BINDING SITE FOR RESIDUE MG A1084

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UN3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4UN3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UN3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UN3)

(-) Exons   (0, 0)

(no "Exon" information available for 4UN3)

(-) 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:RNA  Length:81
                                                                                                                  
                4un3 A    1 AUAACUCAAUUUGUAAAAAAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG   81
                                    10        20        30        40        50        60        70        80 


Chain B from PDB  Type:PROTEIN  Length:1306
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeeeeee......eeeeeeee.....eeeee.eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.................hhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh..........hhhhhhhh..hhhhhhhhhhhh.......hhhhhhhhhhh.......................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhh..eee.......ee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhh....ee..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhh........hhhhhhh........hhhhhhhh......hhhhhhhh...hhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhhh.hhhhhh..hhhhh.hhhhhhhhhh..............hhhhheeee..........hhh.eeee.hhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.ee.....ee...eeee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhh.......eee......eeee..hhhhhhhhhhh....eeee..............................hhhhhh......eeeeeeeeeeeee....eeeeeeeeeeee..hhhhhhhhhhhhhhhh.....hhhhheee....eee.....eeee.....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......ee....ee........hhhhh.eeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4un3 B    4 KYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDGKATAKYFFYSNIMNFFKTEIKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQ 1364
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383||     394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704     ||722       732       742       752       762  ||   782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012|     1039      1049||    1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227      1237   || 1258      1268      1278      1288      1298      1308      1318      1328      1338      1348      1358      
                                                                                                                                                                                                                                                                                                                                                                                                                      384|                                                                                                                                                                                                                                                                                                                                 710|                                           765|                                                                                                                                                                                                                                        1012|                1050|                                                                                                                                                                                  1241|                                                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                       386                                                                                                                                                                                                                                                                                                                                  719                                            776                                                                                                                                                                                                                                         1030                 1059                                                                                                                                                                                   1253                                                                                                               


Chain C from PDB  Type:DNA  Length:28
                                                             
                4un3 C    1 CAATACCATTTTTTACAAATTGAGTTAT   28
                                    10        20        


Chain D from PDB  Type:DNA  Length:11
                                            
                4un3 D    2 AAATGGTATTG   12
                                    11
   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 4UN3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UN3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UN3)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  4un3
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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 4un4 4un5 4zt0 4zt9 5b2r 5b2s 5b2t 5f9r 5fq5 5fw1 5fw2 5fw3 5vw1 5xbl

(-) Related Entries Specified in the PDB File

4un4 CRYSTAL STRUCTURE OF CAS9 BOUND TO PAM-CONTAINING DNA TARGET WITH MISMATCHES AT POSITIONS 1-2
4un5 CRYSTAL STRUCTURE OF CAS9 BOUND TO PAM-CONTAINING DNA TARGET CONTAINING MISMATCHES AT POSITIONS 1-3