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(-) Description

Title :  CRYSTAL STRUCTURE OF SPCAS9 VARIANT VRER BOUND TO SGRNA AND TGCG PAM TARGET DNA
 
Authors :  C. Anders, K. Bargsten, M. Jinek
Date :  11 Feb 16  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase-Dna-Rna Complex, Crispr, Cas9, Endonuclease, Pam, Genome Editing, Rnp, Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Anders, K. Bargsten, M. Jinek
Structural Plasticity Of Pam Recognition By Engineered Variants Of The Rna-Guided Endonuclease Cas9.
Mol. Cell V. 61 895 2016
PubMed-ID: 26990992  |  Reference-DOI: 10.1016/J.MOLCEL.2016.02.020

(-) 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
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    Strain: M1
    Synonym: CAS9 VRER VARIANT, SPCAS9
 
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  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1K11Ligand/IonPOTASSIUM ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREU A:22 , HOH A:2010 , HOH A:2011 , HOH A:2012 , HOH A:2053 , HOH A:2054BINDING SITE FOR RESIDUE MG A1083
02AC2SOFTWAREU A:50 , HOH A:2027 , HOH A:2028 , HOH A:2029 , HOH A:2030 , HOH A:2037BINDING SITE FOR RESIDUE MG A1084
03AC3SOFTWAREA A:68 , HOH A:2051 , GLN B:1350 , HOH B:2075BINDING SITE FOR RESIDUE K B2366
04AC4SOFTWAREGLU B:584 , ARG B:586 , ASN B:588 , HOH B:2042 , HOH B:2043 , HOH B:2044BINDING SITE FOR RESIDUE K B2367
05AC5SOFTWAREA A:65 , U A:66 , HOH A:2045 , HOH A:2046 , HOH A:2049 , THR B:1102BINDING SITE FOR RESIDUE K B2368
06AC6SOFTWAREG A:21 , U A:45 , HOH A:2002 , HOH A:2011 , HOH A:2022BINDING SITE FOR RESIDUE K A1182
07AC7SOFTWARELEU B:623 , THR B:624 , PHE B:626 , TYR B:656 , HOH B:2048 , HOH C:2002BINDING SITE FOR RESIDUE K B2369
08AC8SOFTWAREGLY B:361 , TYR B:362 , GLY B:365 , ALA B:367 , LYS B:401BINDING SITE FOR RESIDUE K B2370
09AC9SOFTWAREILE B:226 , LEU B:229 , GLU B:232BINDING SITE FOR RESIDUE K B2371
10BC1SOFTWAREALA B:640 , PHE B:643BINDING SITE FOR RESIDUE K B2372
11BC2SOFTWAREU A:12 , G A:13BINDING SITE FOR RESIDUE K A1183
12BC3SOFTWAREGLU B:57 , HOH B:2006 , HOH B:2007 , HOH B:2077BINDING SITE FOR RESIDUE K B2373
13BC4SOFTWARELYS B:111 , HOH B:2010BINDING SITE FOR RESIDUE K B2374

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FW3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FW3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FW3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FW3)

(-) Exons   (0, 0)

(no "Exon" information available for 5FW3)

(-) 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
                                                                                                                  
                5fw3 A    1 AUAACUCAAUUUGUAAAAAAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG   81
                                    10        20        30        40        50        60        70        80 


Chain B from PDB  Type:PROTEIN  Length:1322
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeeee......eeeeeeee.....eeeee.eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhh.......hhhhhhhhhhhh......................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhh...ee..........hhhhhhhhhhhh.......hhhhhhhhhhhhhhh....ee..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhh........hhhhhhh........hhhhhhhh......hhhhhh.....hhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhh...........hhhhhhhheeee..........hhh.eeee.hhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.............eeeee.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhh...ee.....ee...eee......eeee..hhhhhhhhhhh....eeee..............................hhhhhh......eeeeeeeeeeeee....eeeeeeeeeeeehhhhhhhhhhhhhhhhhh.....hhhhheee...eeeee...eeeee.....eee......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.......ee....ee........hhhhh.eeeee......eeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fw3 B    3 KKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDEIGKATAKYFFYSNIMNFFKTEITLAEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFVSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASARELQKGNELALPSKYVNFLYLASHNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKEYRSTKEVLDATLIHQSITGLYETRIDLSQL 1365
                                    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|      727       737       747       757       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006     |1031      1041      1051 ||   1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               712|                                             766|                                                                                                                                                                                                                                        1012|                     1053|                                                                                                                                                                                     1241|                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                718                                              776                                                                                                                                                                                                                                         1028                      1056                                                                                                                                                                                      1252                                                                                                                 


Chain C from PDB  Type:DNA  Length:28
                                                             
                5fw3 C    1 CAACCGCATTTTTTACAAATTGAGTTAT   28
                                    10        20        


Chain D from PDB  Type:DNA  Length:11
                                            
                5fw3 D    2 AAATGCGATTG   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 5FW3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FW3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FW3)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

5fw1 CRYSTAL STRUCTURE OF SPYCAS9 VARIANT VQR BOUND TO SGRNA AND TGAG PAM TARGET DNA
5fw2 CRYSTAL STRUCTURE OF SPYCAS9 VARIANT EQR BOUND TO SGRNA AND TGAG PAM TARGET DNA