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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS CAS9 IN COMPLEX WITH SGRNA AND TARGET DNA (TTGAAT PAM)
 
Authors :  H. Nishimasu, R. Ishitani, O. Nureki
Date :  01 Aug 15  (Deposition) - 02 Sep 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Crispr-Cas9, Genome Engineering, Hydrolase-Rna-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Nishimasu, L. Cong, W. X. Yan, F. A. Ran, B. Zetsche, Y. Li, A. Kurabayashi, R. Ishitani, F. Zhang, O. Nureki
Crystal Structure Of Staphylococcus Aureus Cas9
Cell(Cambridge, Mass. ) V. 162 1 2015
PubMed: search  |  Reference-DOI: 10.1016/J.CELL.2015.08.007

(-) Compounds

Molecule 1 - CRISPR-ASSOCIATED ENDONUCLEASE CAS9
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PE-SUMO
    Expression System Strain: BL21(DE3) ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CAS9
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 46170
 
Molecule 2 - RNA (73-MER)
    Chains: B
    Engineered: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: GUIDE RNA
    Synthetic: YES
 
Molecule 3 - DNA (28-MER)
    Chains: C
    Engineered: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: TARGET DNA
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*TP*TP*GP*AP*AP*TP*AP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: NON-TARGET DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2NA5Ligand/IonSODIUM ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:389 , THR A:390 , HOH A:1205 , HOH A:1223 , HOH A:1254 , HOH C:201binding site for residue NA A 1101
2AC2SOFTWARELEU A:592 , SER A:594 , SER A:597 , ILE A:599binding site for residue NA A 1102
3AC3SOFTWAREGLU A:231 , MET A:232 , MET A:234 , HIS A:236binding site for residue NA A 1103
4AC4SOFTWAREU B:11 , G B:12 , HOH B:215 , HOH B:216 , HOH B:217 , HOH C:203binding site for residue NA B 101
5AC5SOFTWAREG B:70binding site for residue PO4 B 102
6AC6SOFTWAREG B:21 , U B:22 , DG C:9binding site for residue EDO B 103
7AC7SOFTWAREHOH A:1222 , DT C:5 , DC C:6 , HOH C:202 , HOH C:204 , HOH D:206binding site for residue NA C 101
8AC8SOFTWAREASN A:885 , HOH C:202 , DG D:3 , DA D:4 , DA D:5binding site for residue EDO D 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CZZ)

(-) 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:PROTEIN  Length:1043
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.................hhhhhhhhhh...............hhhhhhhhhhhhhhh.ee........hhhhhhhhhhhh.......hhhhhhhhhh.hhh.ee..............hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....hhhhhhhhh...........hhhhhhhhhhhhhhh..hhhhhhhhh.........................hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...........hhhhhhhh...eeeee..hhhhhh..hhh.eeeeehhhhhhhh..hhhhhhh......hhhhhhhhhhhhh......hhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh...eeee..............eeeeee.....eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh................eeeeeeee....ee.hhhh......eee....eeeeeeeee..eeeeeeee...eee....eeehhhhhhhhhhhh......eeeeee....eeee..eeeeeeeeee....eeeee....hhhhhhhhh.......eeee.......eeeeee.....eee........ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5czz A    3 RNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKKDGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQSSEDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRLKLVPKKVDLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAREKNSKDAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYSLEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEEASKKGNRTPFQYLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNLVDTRYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKGYKHHAEDALIIANADFIFKEWKKLDKAKKVMENQMFMPEIETEQEYKEIFITPHQIKHIKDFKDYKYSHRVDKKPNRELINDTLYSTRKDDKGNTLIVNNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKVVKLSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKAYEEAKKLKKISNQAEFIASFYNNDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLENMNDKRPPRIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQIIKK 1052
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732||     749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    733|                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     741                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:DNA/RNA  Length:73
                                                                                                          
                5czz B    1 GGAAAUUAGGUGCGCUUGGCGUUUUAGUACUCUGGAAACAGAAUCUACUAAAACAAGGCAAAAUGCCGUGUUU   73
                                    10        20        30        40        50        60        70   


Chain C from PDB  Type:DNA  Length:28
                                                             
                5czz C    1 CTATTCAAGCCAAGCGCACCTAATTTCC   28
                                    10        20        


Chain D from PDB  Type:DNA  Length:8
                                         
                5czz D    1 TTGAATAG    8
   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 5CZZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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        CAS9_STAAU | J7RUA5: 5axw

(-) Related Entries Specified in the PDB File

5axw