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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 :  2.80
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  (6, 21)

Asymmetric/Biological Unit (6, 21)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MG2Ligand/IonMAGNESIUM ION
3MN2Ligand/IonMANGANESE (II) ION
4MSE14Mod. Amino AcidSELENOMETHIONINE
5SPD1Ligand/IonSPERMIDINE
6ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:566 , CYS A:569 , CYS A:602 , ARG A:604 , CYS A:605BINDING SITE FOR RESIDUE ZN A 1201
2AC2SOFTWAREASP A:17 , HIS A:736 , ASP A:739 , HOH A:1302BINDING SITE FOR RESIDUE MN A 1202
3AC3SOFTWAREGLN A:586 , GLY A:588 , GLY A:590 , HOH A:1301 , HOH A:1303 , HOH A:1309BINDING SITE FOR RESIDUE MG A 1203
4AC4SOFTWAREASP A:581 , ASN A:606 , HOH A:1304 , HOH A:1305 , HOH A:1306 , HOH A:1307BINDING SITE FOR RESIDUE MG A 1204
5AC5SOFTWAREMSE A:675 , SER A:704 , ALA A:708 , ALA A:712 , LEU A:754 , ARG A:757 , SER A:758 , ARG A:761 , TRP A:773BINDING SITE FOR RESIDUE SPD A 1205
6AC6SOFTWAREASP A:17 , GLU A:505BINDING SITE FOR RESIDUE MN A 1206
7AC7SOFTWAREHIS A:1074BINDING SITE FOR RESIDUE ACT A 1207

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Val A:256 -Ser A:257
2Ala A:381 -Asp A:382
3Cys A:402 -Ala A:403
4Arg A:508 -Asp A:509
5Asp A:509 -Gly A:510
6Lys A:725 -Gly A:726
7Asp A:822 -Gly A:823
8Gly A:936 -Lys A:937

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OGC)

(-) 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:883
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...eeeeeeeee.....eeeeeeeeeee...........................hhhhhhhhhhhhhh..ee.......ee.hhhhhhhhhhhhhhh.....hhhhhhhhhh.hhh.ee..........hhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh..hhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh................eeee...........hhh.eeeehhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh........hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....................eeee.hhh.hhhhhhh..hhhhhhhhhhh...............eeee..eeee...eeee.................eeee..eeee....eeeeeeeee.....eeeeeeee.hhhhhhh............hhhhhh.hhhhhhhhhh..eeeeeee....eee.......hhhhhhhhhhh....eeeeee.....eeeeee...hhhhh...hhhhhhhhh...eeeehhhhhhh..eee...................ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ogc A    8 SAHHLRVGIDVGTHSVGLATLRVDDHGTPIELLSALSHIHDSGSAVSRVAPDPLPGQGSFRRAPKCDPEFQRFRIISIVANLRISETKGENRPLTADERRHVVTFLTEDSQADLTWVDVAEKLGVHRRDLRGTRSAARPPIDATDRImRQTKISSLKTWWEEADSEQRGAmIRYLYEDPTDSECAEIIAELPEEDQAKLDSLHLPAGRAAYSRESLTALSDHmLATTDDLHEARKRLFGVDDSWAPPAEAINAPVGNPSVDRTLKIVGRYLSAVESmWGTPEVIHVEHVRDGFTSERmADERDKANRRRYNDNQEAmKKIQRDYGKEGYISRGDIVRLDALELQGCACLYCGTTIGYHTCQLDHIVPQAGPGSNNRRGNLVAVCERCNRSKSNTPFAVWAQKCGIPHVGVKEAIGRVRGWRKQTPNTSSEDLTRLKKEVIARLRRTQEDPEIDERSmESVAWmANELHHRIAAAYPETTVmVYRGSITAAARKAAGIDSRINLIGEKGRKDRIDRRHHAVDASVVALmEASVAKTLAERSSLRGEQRLTGKEQTWKQYTGSTVGAREHFEmWRGHmLHLTELFNERLAEDKVYVTQNIRLRLSDGNAHTVNPSKLVSHRLGDGLTVQQIDRACTPALWCALTREKDFDEKNGLPAREDRAIRVHGHEIKSSDYIQVFSKRKKTDSDRDETPFGAIAVRGGFVEIGPSIHHARIYRVEGKKPVYAmLRVFTHDLLSQRHGDLFSAVIPPQSISmRCAEPKLRKAITTGNATYLGWVVVGDELEINVDSFTKYAIGRFLEDFPNTTRWRICGYDTNSKLTLKPIVLAAEGLENPSSAVNEIVELKGWRVAINVLTKVHPTVVRRDALGRPRYSSRSNLPTSWTIE 1101
                                    17        27        37        47 ||    260       270       280       290       300       310       320       330       340  ||   358       368       378       388|      398       408       418       428       438  |    448       458       468       478       488      |498       508       518       528      |538       548       558       568       578       588       598       608       618       628       638       648       658       668      |678  |    688       698|      708       718       728       738       748       758       768       778       788|    | 798       808       818       828       838       848       858       868       878       888       898       908       918       928       938    |  948       958       968  |    978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098   
                                                                    49|                                                                                       343|           366-MSE                389-MSE                                             441-MSE                                               495-MSE              516-MSE            535-MSE                                                                                                                                     675-MSE |               699-MSE                                        746-MSE                                    789-MSE|                                                                                                                                                  943-MSE                     971-MSE                                                                                                                              
                                                                    253                                                                                        352                                                                                                                                                                                                                                                                                                                                      681-MSE                                                                                                          794-MSE
   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 4OGC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:381 - Asp A:382   [ RasMol ]  
    Arg A:508 - Asp A:509   [ RasMol ]  
    Asp A:509 - Gly A:510   [ RasMol ]  
    Asp A:822 - Gly A:823   [ RasMol ]  
    Cys A:402 - Ala A:403   [ RasMol ]  
    Gly A:936 - Lys A:937   [ RasMol ]  
    Lys A:725 - Gly A:726   [ RasMol ]  
    Val A:256 - Ser A:257   [ RasMol ]  
 

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 Related Entries

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        CAS9_ACTNH | J3F2B0: 4oge

(-) Related Entries Specified in the PDB File

4cmp 4cmq 4oge