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 SUBUNIT OF THE CRISPR RNA SILENCING COMPLEX
 
Authors :  A. I. Cocozaki, N. F. Ramia, Y. Shao, C. R. Hale, R. M. Terns, M. P. Terns, H
Date :  15 Nov 11  (Deposition) - 21 Mar 12  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  C
Keywords :  Ferredoxin Fold, Nucleotide-Binding, Polymerase, Cmr Complex, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. I. Cocozaki, N. F. Ramia, Y. Shao, C. R. Hale, R. M. Terns, M. P. Terns, H. Li
Structure Of The Cmr2 Subunit Of The Crispr-Cas Rna Silencing Complex.
Structure V. 20 545 2012
PubMed-ID: 22405013  |  Reference-DOI: 10.1016/J.STR.2012.01.018

(-) Compounds

Molecule 1 - CMR2DHD
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET200D
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 215-871
    Gene: PF1129
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : C

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP C:600 , ASP C:673 , ASP C:674 , CA C:902 , ADP C:904BINDING SITE FOR RESIDUE CA C 901
2AC2SOFTWAREASP C:600 , GLY C:601 , ASP C:673 , CA C:901 , HOH C:1001 , HOH C:1035BINDING SITE FOR RESIDUE CA C 902
3AC3SOFTWARECYS C:448 , CYS C:451 , CYS C:478 , CYS C:481BINDING SITE FOR RESIDUE ZN C 903
4AC4SOFTWAREVAL C:229 , ILE C:233 , SER C:246 , SER C:250 , ASN C:300 , TYR C:669 , ASP C:674 , CA C:901 , HOH C:1001 , HOH C:1025BINDING SITE FOR RESIDUE ADP C 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UNG)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val C:216 -Lys C:217
2Val C:227 -Pro C:228
3Tyr C:271 -Pro C:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UNG)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GGDEFPS50887 GGDEF domain profile.CMR2_PYRFU592-752  1C:592-752

(-) Exons   (0, 0)

(no "Exon" information available for 3UNG)

(-) 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 C from PDB  Type:PROTEIN  Length:548
 aligned with CMR2_PYRFU | Q8U1S6 from UniProtKB/Swiss-Prot  Length:871

    Alignment length:657
                                   224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       
           CMR2_PYRFU   215 SVKDPTLLRIKIVPVQPFIANSRKQLDLWASSHLLSMLMYKALEVIVDKFGPEHVIYPSLRDQPFFLKFYLGENIGDEILVANLPNKALAIVSGKEAEKIEEEIKKRIRDFLLQLYREAVDWAVENGVVKVDRSEKDSMLKEAYLKIVREYFTVSITWVSLSEKEDIYQVTENAGLSDEDVKKWLKFAEKKENSRVLERIAIYPLLVKILDSLGERKVTEERFEKSEQLKGWKCHVCGENLAIFGDMYDHDNLKSLWLDEEPLCPMCLIKRYYPVWIRSKTGQKIRFESVVDVALLYKNWRKIFDEKYGKDLVSKAREVSEDFVKDNMLVDSDLYYSSTWESGLSKKLKNKKEIDEEKVKEVVDFLNAAYKEIGNPPKYYAILVMDGDDMGKVISGEVLGEISTRIHPNIRDYVEIPEAKYYSTPQVHVAISQALANFSIREVRSVVKDEGLLIYAGGDDVLAILPVDKALEVAYKIRKEFGKSFENGSLLPGWKLSAGILIVHYKHPLYDALEKARDLLNNKAKNVPGKDTLAIGLLKRSGSYYISLVGWELIRVFYNSELRKKLLEEKGGVGKRFIYHVLREVDTWPKVGIDEMLKFEVIRHIRGRNKEETKELREKIYGEIKDLLEHVRGNNEVEKVRGLFTFLKIITDAEVFP 871
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.....hhhhhhhh....hhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhh.eeeeeeee.---------------------------------------.hhhhhhhhhhhhhhhhh...---------..................hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..----------.hhhhhhhhhhhhhhhhhhh....eeeeeeeee....--------------------------------.hhhhhhhhhhhhhhhhhhhhhhhh...eeeee...eeeeeeehhhhhhhhhhhhhhhhh.---------..eeeeeeeee...hhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeeehhhhhhhhhhhhhhhhh------.hhhhhhhhhhh......hhhhhhhhhhhhh.----..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGDEF  PDB: C:592-752 UniProt: 592-752                                                                                                                           ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ung C 215 SVKDPTLLRIKIVPVQPFIANSRKQLDLWASSHLLSMLMYKALEVIVDKFGPEHVIYPSLRDQPFFLKFYLGENIGDEILVANLPNKALAIVSGKEAEKIEEEIKKRIRDFLLQLYREAVDWAVENGVVKVDRSEKDSMLKEAYLKIVREYFTVSITWVSL---------------------------------------AIYPLLVKILDSLGERKVTEE---------GWKCHVCGENLAIFGDMYDHDNLKSLWLDEEPLCPMCLIKRYYPVWIRSKTGQKIRFESVVDVALLYKNWRKIFDEKYGKDLVSKAREVSEDFVKDNMLVDSDLYYSSTWESGL----------DEEKVKEVVDFLNAAYKEIGNPPKYYAILVMDGDDMG--------------------------------TPQVHVAISQALANFSIREVRSVVKDEGLLIYAGGDDVLAILPVDKALEVAYKIRKEFGKS---------WKLSAGILIVHYKHPLYDALEKARDLLNNKAKNVPGKDTLAIGLLKRSGSYYISLVGWELIRVFYNSELRKKLL------GKRFIYHVLREVDTWPKVGIDEMLKFEVIRHI----KEETKELREKIYGEIKDLLEHVRGNNEVEKVRGLFTFLKIITDAEVFP 871
                                   224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374|        -         -         -         -|      424       434|        -|      454       464       474       484       494       504       514       524       534       544       554   |     -    |  574       584       594       604|        -         -         -   |   644       654       664       674       684       694   |     -   |   714       724       734       744       754       764       774      |  -   |   794       804       814    |  824       834       844       854       864       
                                                                                                                                                                                          375                                     415                 435       445                                                                                                              558        569                                 605                              638                                                         698       708                                                                      781    788                            819  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 3UNG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UNG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UNG)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (CMR2_PYRFU | Q8U1S6)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ 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
    Tyr C:271 - Pro C:272   [ RasMol ]  
    Val C:216 - Lys C:217   [ 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
  3ung
    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
 
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)

 Related Entries

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

UniProtKB/Swiss-Prot
        CMR2_PYRFU | Q8U1S6: 3ur3 3w2v 3w2w 3x1l 4doz 4h4k 4w8y

(-) Related Entries Specified in the PDB File

3ur3