Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CAMPYLOBACTER JEJUNI CAS9 IN COMPLEX WITH SGRNA AND TARGET DNA (AGAAACC PAM)
 
Authors :  M. Yamada, Y. Watanabe, H. Hirano, T. Nakane, R. Ishitani, H. Nishimasu
Date :  31 Jan 17  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Crispr-Cas9, Rna, Dna, Complex, Nuclease, Hydrolase-Rna-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Yamada, Y. Watanabe, J. S. Gootenberg, H. Hirano, F. A. Ran, T. Nakane, R. Ishitani, F. Zhang, H. Nishimasu, O. Nureki
Crystal Structure Of The Minimal Cas9 From Campylobacter Jejuni Reveals The Molecular Diversity In The Crispr-Cas9 Systems
Mol. Cell V. 65 1109 2017
PubMed-ID: 28306506  |  Reference-DOI: 10.1016/J.MOLCEL.2017.02.007

(-) Compounds

Molecule 1 - CRISPR-ASSOCIATED ENDONUCLEASE CAS9
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-480, 642-984
    Gene: CAS9, CJ1523C
    Organism Taxid: 192222
    Other Details: CJCAS9-DHNH
    Strain: ATCC 700819 / NCTC 11168
 
Molecule 2 - SGRNA
    Chains: B
    Engineered: YES
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 197
    Synthetic: YES
 
Molecule 3 - TARGET DNA STRAND
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - NON-TARGET DNA STRAND
    Chains: D
    Engineered: YES
    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  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:57 , G B:18 , G B:19 , HOH B:250 , HOH B:264binding site for residue EDO B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X2G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5X2G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X2G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X2G)

(-) Exons   (0, 0)

(no "Exon" information available for 5X2G)

(-) 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:749
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...eeeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh......hhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh...hhhhhhhhhh.........................hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.......hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhheeehhhhhhh............eeeehhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhh.........hhhhhhhhhhhhhh..hhhhhhhhhh..............hhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.........eeeeehhhhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhh..eee..eee......eeeeeee.....eeeeeehhhhhhhh....ee............ee....eeeeeee....eeeee.......eeeeeeeee....eeeee.........hhhhhhhh........eeeeee.....eeeeeee.....eee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x2g A   1 MARILAFDIGISSIGWAFSENDELKDCGVRIFTKGESLALPRRLARSARKRLARRKARLNHLKHLIANEFKLNYEDYQSFDESLAKAYKGSLISPYELRFRALNELLSKQDFARVILHIAKRRGYDDIKNKEKGAILKAIKQNEEKLANYQSVGEYLYKEYFQKFKENSKEFTNVRNKKESYERCIAQSFLKDELKLIFKKQREFGFSFSKKFEEEVLSVAFYKRALKDFSHLVGNCSFFTDEKRAPKNSPLAFMFVALTRIINLLNNLKNTEGILYTKDDLNALLNEVLKNGTLTYKQTKKLLGLSDDYEFKGEKGTYFIEFKKYKEFISQDDLNEIAKDITLIKDEIKLKKALAKYDLNQNQIDSLSKLEFKDHLNISFKALKLVTPLMLEGKKYDEACNELNLKVAINEDKKDFLPAFNETYYKDEVTNPVVLRAIKEYRKVLNALLKKYGKVHKINIELGGGYIARLVLNYTKDYLDFLPLSDVHVEAKSGMLTSALRHTWGFSAKDRNNHLHHAIDAVIIAYRQKVLDKIDEIFVSKPERKKPSGALHEETFRKEEEFYQSYGGKEGVLKALELGKIRKVNGKIVKNGDMFRVDIFKHKKTNKFYAVPIYTMDFALKVLPNKAVARSKKGEIKDWILMDENYEFCFSLYKDSLILIQTKDMQEPEFVYYNAFTSSTVSLIVSKHDNKFETLSKNQKILFKNANEKEVIAKSIGIQNLKVFEKYIVSALGEVTKAEFRQREDFKK 984
                                    10        20        30   ||   46        56        66        76        86        96       106       116       126       136|      149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339|      357       367       377       387       397       407       417       427       437       447       457       467       477   ||  645       655      |679       689       699       709      |765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975         
                                                            34|                                                                                            136|                                                                                                                                                                                                    339|                                                                                                                                  481|                   662|                                    716|                                                                                                                                                                                                                             
                                                             41                                                                                             140                                                                                                                                                                                                     348                                                                                                                                   640                    677                                     763                                                                                                                                                                                                                             


Chain B from PDB  Type:RNA  Length:93
                                                                                                                             
                 5x2g B   1 GGAAAUUAGGUGCGCUUGGCGUUUUAGUCCCUGAAAAGGGACUAAAAUAAAGAGUUUGCGGGACUCUGCGGGGUUACAAUCCCCUAAAACCGC  93
                                    10        20        30        40        50        60        70        80        90   


Chain C from PDB  Type:DNA  Length:28
                                                            
                 5x2g C  -7 CGGTTTCTGCCAAGCGCACCTAATTTCC  20
                                     2        12        


Chain D from PDB  Type:DNA  Length:8
                                        
                 5x2g D   1 AGAAACCG   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 5X2G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X2G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X2G)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5x2g)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5x2g
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CAS9_CAMJE | Q0P897
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CAS9_CAMJE | Q0P897
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CAS9_CAMJE | Q0P897: 5x2h

(-) Related Entries Specified in the PDB File

5x2h