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(-) 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 :  21 Nov 11  (Deposition) - 21 Mar 12  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
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  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP C:600 , GLY C:601 , MET C:604 , ASP C:673 , HOH C:1029BINDING SITE FOR RESIDUE CA C 901
2AC2SOFTWAREASP C:600 , ASP C:673 , ASP C:674 , HOH C:1029BINDING SITE FOR RESIDUE CA C 902
3AC3SOFTWARECYS C:448 , CYS C:451 , ASN C:454 , CYS C:478 , CYS C:481BINDING SITE FOR RESIDUE ZN C 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UR3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr C:271 -Pro C:272
2Lys C:662 -Asp C:663

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UR3)

(-) 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 3UR3)

(-) 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:656
                                   225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865      
           CMR2_PYRFU   216 VKDPTLLRIKIVPVQPFIANSRKQLDLWASSHLLSMLMYKALEVIVDKFGPEHVIYPSLRDQPFFLKFYLGENIGDEILVANLPNKALAIVSGKEAEKIEEEIKKRIRDFLLQLYREAVDWAVENGVVKVDRSEKDSMLKEAYLKIVREYFTVSITWVSLSEKEDIYQVTENAGLSDEDVKKWLKFAEKKENSRVLERIAIYPLLVKILDSLGERKVTEERFEKSEQLKGWKCHVCGENLAIFGDMYDHDNLKSLWLDEEPLCPMCLIKRYYPVWIRSKTGQKIRFESVVDVALLYKNWRKIFDEKYGKDLVSKAREVSEDFVKDNMLVDSDLYYSSTWESGLSKKLKNKKEIDEEKVKEVVDFLNAAYKEIGNPPKYYAILVMDGDDMGKVISGEVLGEISTRIHPNIRDYVEIPEAKYYSTPQVHVAISQALANFSIREVRSVVKDEGLLIYAGGDDVLAILPVDKALEVAYKIRKEFGKSFENGSLLPGWKLSAGILIVHYKHPLYDALEKARDLLNNKAKNVPGKDTLAIGLLKRSGSYYISLVGWELIRVFYNSELRKKLLEEKGGVGKRFIYHVLREVDTWPKVGIDEMLKFEVIRHIRGRNKEETKELREKIYGEIKDLLEHVRGNNEVEKVRGLFTFLKIITDAEVFP 871
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.....hhhhhhhh....hhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhheeeeeeeee.---------------------------------------.hhhhhhhhhhhhhhhhhhh.---------..................hhhhhhh........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhhh..----------.hhhhhhhhhhhhhhhhhhh....eeeeeeeee....--------------------------------.hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeee..hhhhhhhhhhhhhhhh---------..eeeeeeeee...hhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeeehhhhhhhhhhhhhhhh.-----..hhhhhhhhhhh......hhhhhhhhhhhhhh----..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGDEF  PDB: C:592-752 UniProt: 592-752                                                                                                                           ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ur3 C 216 VKDPTLLRIKIVPVQPFIANSRKQLDLWASSHLLSMLMYKALEVIVDKFGPEHVIYPSLRDQPFFLKFYLGENIGDEILVANLPNKALAIVSGKEAEKIEEEIKKRIRDFLLQLYREAVDWAVENGVVKVDRSEKDSMLKEAYLKIVREYFTVSITWVSL---------------------------------------AIYPLLVKILDSLGERKVTEE---------GWKCHVCGENLAIFGDMYDHDNLKSLWLDEEPLCPMCLIKRYYPVWIRSKTGQKIRFESVVDVALLYKNWRKIFDEKYGKDLVSKAREVSEDFVKDNMLVDSDLYYSSTWESGL----------DEEKVKEVVDFLNAAYKEIGNPPKYYAILVMDGDDMG--------------------------------TPQVHVAISQALANFSIREVRSVVKDEGLLIYAGGDDVLAILPVDKALEVAYKIRKEFGKS---------WKLSAGILIVHYKHPLYDALEKARDLLNNKAKNVPGKDTLAIGLLKRSGSYYISLVGWELIRVFYNSELRKKLL-----VGKRFIYHVLREVDTWPKVGIDEMLKFEVIRHI----KEETKELREKIYGEIKDLLEHVRGNNEVEKVRGLFTFLKIITDAEVFP 871
                                   225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375         -         -         -       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555  |      -   |   575       585       595       605         -         -         -  |    645       655       665       675       685       695  |      -  |    715       725       735       745       755       765       775     |   - |     796       806       816   |   825       835       845       855       865      
                                                                                                                                                                                         375                                     415                 435       445                                                                                                              558        569                                 605                              638                                                         698       708                                                                      781   788                             820  824
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3UR3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UR3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UR3)

(-) 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.

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  Cis Peptide Bonds
    Lys C:662 - Asp C:663   [ RasMol ]  
    Tyr C:271 - Pro C:272   [ RasMol ]  
 

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  CMR2_PYRFU | Q8U1S6
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3ung THE SAME PROTEIN, NOT BOUND TO ADP