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 :  STRUCTURE OF THE CMR2-CMR3 SUBCOMPLEX OF THE CMR RNA-SILENCING COMPLEX
 
Authors :  Y. Shao, A. I. Cocozaki, N. F. Ramia, R. M. Terns, M. P. Terns, H. Li
Date :  17 Sep 12  (Deposition) - 06 Mar 13  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Ferredoxin, Palm, Ramp, Repeat Associated Mysterious Protein, Polymerase, Nuclease, Rna-Interference, Cmr Proteins Crispr Rna, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shao, A. I. Cocozaki, N. F. Ramia, R. M. Terns, M. P. Terns, H. Li
Structure Of The Cmr2-Cmr3 Subcomplex Of The Cmr Rna Silencing Complex.
Structure V. 21 376 2013
PubMed-ID: 23395183  |  Reference-DOI: 10.1016/J.STR.2013.01.002

(-) Compounds

Molecule 1 - CRISPR SYSTEM CMR SUBUNIT CMR3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET200D
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CMR3 (UNP RESIDUES 1-322)
    Gene: CMR3, PF1128
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1
    Synonym: CRISPR TYPE III-B/RAMP MODULE-ASSOCIATED PROTEIN CMR3
 
Molecule 2 - CRISPR SYSTEM CMR SUBUNIT CMR2
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CMR2DHD (UNP RESIDUES 215-871)
    Gene: CMR2, PF1129
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1
    Synonym: CRISPR-ASSOCIATED PROTEIN CAS10/CMR2, SUBTYPE III-B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2NA2Ligand/IonSODIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:111 , VAL C:229 , GLN C:230 , ILE C:233 , SER C:246 , LEU C:249 , ASN C:300 , TYR C:669 , ASP C:674 , NA C:903BINDING SITE FOR RESIDUE ATP C 901
2AC2SOFTWARECYS C:448 , CYS C:451 , CYS C:478 , CYS C:481BINDING SITE FOR RESIDUE ZN C 902
3AC3SOFTWAREATP C:901 , HOH C:1001BINDING SITE FOR RESIDUE NA C 903
4AC4SOFTWAREASP C:600 , GLY C:601 , MET C:604 , ASP C:673BINDING SITE FOR RESIDUE NA C 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H4K)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Leu A:169 -Arg A:170
2Val C:227 -Pro C:228
3Tyr C:271 -Pro C:272
4Asp C:602 -Asp C:603
5Met C:604 -Gly C:605
6Ser C:703 -Leu C:704
7Gly C:707 -Trp C:708
8Lys C:784 -Gly C:785

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H4K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H4K)

(-) Exons   (0, 0)

(no "Exon" information available for 4H4K)

(-) 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhhhhhhhhhh.......eeeeeeeee..eeeee....eeee..eeee...eee..eee..........eeehhhhhhhhh....eee...........eeeeeee....hhhhhhhh.eeee....eeee......hhhhh....eeeeeeeee...ee.hhhhhhhhhhhhh...eeeeeee....eee..ee....ee...eeee....eeeeeeeeeee...eee...hhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h4k A   3 VTFTPYDVLIPLPQTVAGAIRTLLFYEEPEFTLVGIAIGTEKGRIYPLPFNIIKSEKFYKVVNPGRFLGKLILPPKGKYKSGYVTESILEKYLKGELKEVEENKVIRILRIEKIYAWIEDPGCGIKDILSSYEFLTLGSRVAFVEVDDKTPDIFNRELGSTKKALFYFSTPTIGKVGEIVQELEKRLNAKIDDYLLVSSRPTAISGWDMHEKKPKGTKFAIPPGSVLFVEFKEEVEVPPYIKLGKLKKLGYGLALGGIW 321
                                    32        42     || 63        73        83        93       103       113       123       133       170       180       190       202       212       222       232       242       252       262       272       282       292       302       312         
                                   11|              48|                                                                              141|                          198|                                                                                                                        
                                    32               60                                                                               169                           201                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:604
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.....hhhhhhhh....hhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhheeeeeeee.....hhhhhhhhh....hhhhhh.....hhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeeeee..hhhhhhhhhhhhhhhhh.........eeeeeeeeee...hhhhhhhhhhhhhhhh........eeeeeee.....eeeeeeehhhhhhhh.hhhhhhhhh.......hhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h4k C 213 ALSVKDPTLLRIKIVPVQPFIANSRKQLDLWASSHLLSMLMYKALEVIVDKFGPEHVIYPSLRDQPFFLKFYLGENIGDEILVANLPNKALAIVSGKEAEKIEEEIKKRIRDFLLQLYREAVDWAVENGVVKVDRSEKDSMLKEAYLKIVREYFTVSITWVSLSEKEDIYQVTENAGLSDEDVKKWLKFAAIYPLLVKILDSLGERKVTEERFEKSEQLKGWKCHVCGENLAIFGDMYDHDNLKSLWLDEEPLCPMCLIKRYYPVWIRSKTGQKIRFESVVDVALLYKNWRKIFDEKYGKDLVSKAREVSEDFVKDNMLVDSDLYYSSTWESGLSDEEKVKEVVDFLNAAYKEIGNPPKYYAILVMDGDDMGKVTPQVHVAISQALANFSIREVRSVVKDEGLLIYAGGDDVLAILPVDKALEVAYKIRKEFGKSFENGSLLPGWKLSAGILIVHYKHPLYDALEKARDLLNNKAKNVPGKDTLAIGLLKRSGSYYISLVGWELIRVFYNSELRKKLLEEKGGVGKRFIYHVLREVDTWPKVGIDEMLKFEVIRHIKEETKELREKIYGEIKDLLEHVRGNNEVEKVRGLFTFLKIITDAEVFP 871
                                   222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402|      424       434       444       454       464       474       484       494       504       514       524       534       544       554    || 573       583       593       603   ||  643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813     ||827       837       847       857       867    
                                                                                                                                                                                                                       402|                                                                                                                                             559|                                   607|                                                                                                                                                                                  819|                                               
                                                                                                                                                                                                                        415                                                                                                                                              569                                    638                                                                                                                                                                                   824
   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 4H4K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H4K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H4K)

(-) Gene Ontology  (5, 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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp C:602 - Asp C:603   [ RasMol ]  
    Gly C:707 - Trp C:708   [ RasMol ]  
    Leu A:169 - Arg A:170   [ RasMol ]  
    Lys C:784 - Gly C:785   [ RasMol ]  
    Met C:604 - Gly C:605   [ RasMol ]  
    Ser C:703 - Leu C:704   [ RasMol ]  
    Tyr C:271 - Pro C:272   [ RasMol ]  
    Val C:227 - Pro C:228   [ RasMol ]  
 

(-) 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
  4h4k
    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
  CMR2_PYRFU | Q8U1S6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CMR3_PYRFU | Q8U1S7
    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
  CMR2_PYRFU | Q8U1S6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CMR3_PYRFU | Q8U1S7
    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
        CMR2_PYRFU | Q8U1S6: 3ung 3ur3 3w2v 3w2w 3x1l 4doz 4w8y
        CMR3_PYRFU | Q8U1S7: 3w2v 3w2w 3x1l

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4H4K)