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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TYPE II-C CAS9 ENZYME FROM ACTINOMYCES NAESLUNDII
 
Authors :  F. Jiang, E. Ma, S. Lin, J. A. Doudna
Date :  15 Jan 14  (Deposition) - 12 Feb 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Crispr-Cas, Cas9, Hnh, Ruvc, Rna-Guided Dna Endonuclease, Cytoplasmic, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Jinek, F. Jiang, D. W. Taylor, S. H. Sternberg, E. Kaya, E. Ma, C. Anders, M. Hauer, K. Zhou, S. Lin, M. Kaplan, A. T. Iavarone, E. Charpentier, E. Nogales, J. A. Doudna
Structures Of Cas9 Endonucleases Reveal Rna-Mediated Conformational Activation.
Science V. 343 47997 2014
PubMed-ID: 24505130  |  Reference-DOI: 10.1126/SCIENCE.1247997

(-) Compounds

Molecule 1 - HNH ENDONUCLEASE DOMAIN PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Gene: HMPREF1129_2620
    Organism Scientific: ACTINOMYCES NAESLUNDII
    Organism Taxid: 1115803
    Strain: HOWELL 279

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2SPD2Ligand/IonSPERMIDINE
3ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:566 , CYS A:569 , CYS A:602 , CYS A:605BINDING SITE FOR RESIDUE ZN A 1201
2AC2SOFTWAREASP A:581 , ASN A:606 , HOH A:1637 , HOH A:1638 , HOH A:1639 , HOH A:1640BINDING SITE FOR RESIDUE MG A 1202
3AC3SOFTWAREASP A:17 , GLU A:505 , HOH A:1643BINDING SITE FOR RESIDUE MG A 1203
4AC4SOFTWAREGLN A:586 , GLY A:588 , GLY A:590 , HOH A:1634 , HOH A:1635 , HOH A:1636BINDING SITE FOR RESIDUE MG A 1204
5AC5SOFTWAREALA A:708 , LYS A:711 , ALA A:712 , LEU A:754 , ARG A:757 , SER A:758 , ARG A:761 , TRP A:773BINDING SITE FOR RESIDUE SPD A 1205
6AC6SOFTWAREARG A:817 , SER A:821 , PRO A:924 , SER A:925 , ILE A:926 , HIS A:927 , HOH A:1378BINDING SITE FOR RESIDUE SPD A 1206

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Val A:156 -Glu A:157
2Ala A:229 -Arg A:230
3Gln A:231 -Gly A:232
4Gly A:232 -Val A:233
5Ala A:248 -Asp A:249
6Ser A:254 -Ala A:255
7Ser A:257 -Arg A:258
8Lys A:298 -Gly A:299
9Cys A:402 -Ala A:403
10Asp A:509 -Gly A:510
11Lys A:725 -Gly A:726
12Arg A:727 -Lys A:728

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OGE)

(-) 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:977
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eeeeeeeee.....eeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.................................hhhhhhhhhhhh.............................hhhhhhhhhhhhhhh.eee.....eee.hhhhhhhhhhhhhhh.....hhhhhhhhhh.hhh.ee..............hhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhh....hhhhhh........hhhhhh..........hhhhhhhhhhhhhhh..hhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh................eeee...........hhh.eeeehhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....................eeee.hhh.hhhhhhh..hhhhhhhhhh................eeee..eeee...eeee.................eeee..eeee....eeeeeeeee.....eeeeeeee.hhhhhhh............hhhhhh.hhhhhhhhhh..eeeeeee....eee.......hhhhhhhhhhh....eeeeeeeee..eeeeee...hhhhh...hhhhhhhhh...eeeehhhhhhh..eee...................ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4oge A   10 HHLRVGIDVGTHSVGLATLRVDDHGTPIELLSALSHIHDLSGIARRARRLLHHRRTQLQQLDEVLRDLGFPIPSMAVRHIARHRGWRNPYSKVESLLSPAEESPFMKRKICARQGVSPDVCKQLLRAVFKADSPRGSAVSRVAPDPLPGQGSFRRAPKCDPEFQRFRIISIVANLRISETKGENRPLTADERRHVVTFLTEDSQADLTWVDVAEKLGVHRRDLRGTAVHTRSAARPPIDATDRIMRQTKISSLKTWWEEADSEQRGAMIRYLYEDPTDSECAEIIAELPEEDQAKLDSLHLPAGRAAYSRESLTALSDHMLATTDDLHEARKRLFGVDDSWAPPAEAINAPVGNPSVDRTLKIVGRYLSAVESMWGTPEVIHVEHVRDGFTSERMADERDKANRRRYNDNQEAMKKIQRDYGKEGYISRGDIVRLDALELQGCACLYCGTTIGYHTCQLDHIVPQAGPGSNNRRGNLVAVCERCNRSKSNTPFAVWAQKCGIPHVGVKEAIGRVRGWRKQTSSEDLTRLKKEVIARLRRTQEDPEIDERSMESVAWMANELHHRIAAAYPETTVMVYRGSITAAARKAAGIDSRINLIGEKGRKDRIDRRHHAVDASVVALMEASVAKTLAERSSLRGEQRLTGKEQTWKQYTGSTVGAREHFEMWRGHMLHLTELFNERLAEDKVYVTQNIRLRLSDGNAHTVNPSKLVSHRLGDGLTVQQIDRACTPALWCALTREKDFDEKNGLPAREDRAIRVHGHEIKSSDYIQVFSKRKKTDSDRDETPFGAIAVRGGFVEIGPSIHHARIYRVEGKKPVYAMLRVFTHDLLSQRHGDLFSAVIPPQSISMRCAEPKLRKAITTGNATYLGWVVVGDELEINVDSFTKYAIGRFLEDFPNTTRWRICGYDTNSKLTLKPIVLAAEGLENPSSAVNEIVELKGWRVAINVLTKVHPTVVRRDALGRPRYSSRSNLPTSWTIE 1101
                                    19        29        39        65        75        85        95  ||   143       153       163      |227       237       247       257       267       277       287       297       307       317       327       337       347|      361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641||     654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094       
                                                                 48|                               98|                              170|                                                                                                                       347|                                                                                                                                                                                                                                                                                               642|                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                  65                               137                               225                                                                                                                        352                                                                                                                                                                                                                                                                                                646
   Legend:   → Mismatch (orange background)
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  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 4OGE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:229 - Arg A:230   [ RasMol ]  
    Ala A:248 - Asp A:249   [ RasMol ]  
    Arg A:727 - Lys A:728   [ RasMol ]  
    Asp A:509 - Gly A:510   [ RasMol ]  
    Cys A:402 - Ala A:403   [ RasMol ]  
    Gln A:231 - Gly A:232   [ RasMol ]  
    Gly A:232 - Val A:233   [ RasMol ]  
    Lys A:298 - Gly A:299   [ RasMol ]  
    Lys A:725 - Gly A:726   [ RasMol ]  
    Ser A:254 - Ala A:255   [ RasMol ]  
    Ser A:257 - Arg A:258   [ RasMol ]  
    Val A:156 - Glu A:157   [ RasMol ]  
 

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  4oge
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  CAS9_ACTNH | J3F2B0
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAS9_ACTNH | J3F2B0: 4ogc

(-) Related Entries Specified in the PDB File

4cmp
4cmq
4ogc THE SAME PROTEIN SOAKING WITH MN++ IONS.