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(-) Description

Title :  CRYSTAL STRUCTURE OF SPCAS9 VARIANT EQR BOUND TO SGRNA AND TGAG 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 :  2.68
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 EQR 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, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1K10Ligand/IonPOTASSIUM ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:21 , HOH A:2001 , HOH A:2022 , HOH A:2023 , HOH A:2037 , HOH A:2038BINDING SITE FOR RESIDUE K A1182
02AC2SOFTWAREU A:12 , G A:13 , HOH A:2012BINDING SITE FOR RESIDUE K A1183
03AC3SOFTWAREU A:50 , HOH A:2052 , HOH A:2053 , HOH A:2054 , HOH A:2055 , HOH A:2064BINDING SITE FOR RESIDUE MG A1084
04AC4SOFTWAREA A:68 , HOH A:2081 , GLN B:1350 , HOH B:2075 , HOH B:2105BINDING SITE FOR RESIDUE K B2366
05AC5SOFTWAREGLU B:584 , ARG B:586 , ASN B:588 , HOH B:2052 , HOH B:2053BINDING SITE FOR RESIDUE K B2367
06AC6SOFTWAREA A:65 , U A:66 , HOH A:2072 , HOH A:2073 , HOH A:2077 , HOH A:2078 , THR B:1102BINDING SITE FOR RESIDUE K B2368
07AC7SOFTWARELEU B:623 , THR B:624 , PHE B:626 , TYR B:656 , HOH B:2057 , HOH C:2007BINDING SITE FOR RESIDUE K B2369
08AC8SOFTWAREGLY B:361 , TYR B:362 , GLY B:365 , GLY B:366 , ALA B:367BINDING SITE FOR RESIDUE K B2370
09AC9SOFTWAREALA B:640 , PHE B:643BINDING SITE FOR RESIDUE K B2371
10BC1SOFTWAREHOH A:2073 , THR B:1102 , HOH B:2001 , HOH B:2007BINDING SITE FOR RESIDUE K B2372
11BC2SOFTWARELYS B:111 , HOH B:2011 , HOH B:2012 , HOH B:2013BINDING SITE FOR RESIDUE K B2373
12BC3SOFTWAREHOH A:2021 , HOH A:2023 , HOH A:2024 , HOH A:2087BINDING SITE FOR RESIDUE MG A1083

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FW2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FW2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FW2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FW2)

(-) Exons   (0, 0)

(no "Exon" information available for 5FW2)

(-) 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
                                                                                                                  
                5fw2 A    1 AUAACUCAAUUUGUAAAAAAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG   81
                                    10        20        30        40        50        60        70        80 


Chain B from PDB  Type:PROTEIN  Length:1316
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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...............hhhhhhhhhhhhhhhhh..........hhhhhhhh..hhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhh............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhh..eee.......ee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eee.........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhh........hhhhhh.........hhhhhhhh......hhhhhhhh...hhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhh...........hhhhhhhheeee..........hhh.eeee.hhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.............eeeee.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhh........eee......eeee..hhhhhhhhhhh....eeee..............................hhhhhh......eeeeeeeeeeeee....eeeeeeeeeeeehhhhhhhhhhhhhhhhhh.ee..hhhhheee....eee.hhh.eeee.....eee......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......eee..eee........hhhhh.eeeee......eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fw2 B    3 KKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDGKATAKYFFYSNIMNFFKTEITKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFESPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKQYRSTKEVLDATLIHQSITGLYETRIDLSQL 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||     726       736       746       756       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1032      1042      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239 ||   1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                713|                                            765|                                                                                                                                                                                                                                         1012|                 1051|                                                                                                                                                                                  1241|                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 718                                             775                                                                                                                                                                                                                                          1030                  1059                                                                                                                                                                                   1252                                                                                                                 


Chain C from PDB  Type:DNA  Length:28
                                                             
                5fw2 C    1 CAATCTCATTTTTTACAAATTGAGTTAT   28
                                    10        20        


Chain D from PDB  Type:DNA  Length:11
                                            
                5fw2 D    2 AAATGAGATTG   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 5FW2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FW2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FW2)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  5fw2
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  CAS9_STRP1 | Q99ZW2
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  3.1.-.-
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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 5fw3 5vw1 5xbl

(-) Related Entries Specified in the PDB File

5fw1 CRYSTAL STRUCTURE OF SPYCAS9 VARIANT VQR BOUND TO SGRNA AND TGAG PAM TARGET DNA
5fw3 CRYSTAL STRUCTURE OF SPYCAS9 VARIANT VRER BOUND TO SGRNA AND TGCG PAM TARGET DNA