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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CMR2DHD-CMR3 SUBCOMPLEX BOUND TO 3'-AMP
 
Authors :  T. Numata, T. Osawa
Date :  06 Dec 12  (Deposition) - 16 Oct 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ferredoxin-Like Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Osawa, H. Inanaga, T. Numata
Crystal Structure Of The Cmr2-Cmr3 Subcomplex In The Crispr-Cas Rna Silencing Effector Complex.
J. Mol. Biol. V. 425 3811 2013
PubMed-ID: 23583914  |  Reference-DOI: 10.1016/J.JMB.2013.03.042

(-) Compounds

Molecule 1 - CRISPR SYSTEM CMR SUBUNIT CMR2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 216-871
    Gene: CMR2, PF1129
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: DSM 3638
    Synonym: CRISPR-ASSOCIATED PROTEIN CAS10/CMR2, SUBTYPE III-B
 
Molecule 2 - CRISPR SYSTEM CMR SUBUNIT CMR3
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CMR3, PF1128
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: DSM 3638
    Synonym: CRISPR TYPE III-B/RAMP MODULE-ASSOCIATED PROTEIN CMR3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
13AM1Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL] DIHYDROGEN PHOSPHATE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:448 , CYS A:451 , CYS A:478 , CYS A:481BINDING SITE FOR RESIDUE ZN A 901
2AC2SOFTWAREVAL A:229 , GLN A:230 , ILE A:233 , SER A:246 , LEU A:249 , ASN A:300 , LYS A:301 , TYR A:669 , ASP A:674 , HOH A:1002 , LYS B:111BINDING SITE FOR RESIDUE 3AM A 902

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:54 -B:183

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:227 -Pro A:228
2Tyr A:271 -Pro A:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W2V)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3W2V)

(-) 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:602
 aligned with CMR2_PYRFU | Q8U1S6 from UniProtKB/Swiss-Prot  Length:871

    Alignment length:655
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866     
           CMR2_PYRFU   217 KDPTLLRIKIVPVQPFIANSRKQLDLWASSHLLSMLMYKALEVIVDKFGPEHVIYPSLRDQPFFLKFYLGENIGDEILVANLPNKALAIVSGKEAEKIEEEIKKRIRDFLLQLYREAVDWAVENGVVKVDRSEKDSMLKEAYLKIVREYFTVSITWVSLSEKEDIYQVTENAGLSDEDVKKWLKFAEKKENSRVLERIAIYPLLVKILDSLGERKVTEERFEKSEQLKGWKCHVCGENLAIFGDMYDHDNLKSLWLDEEPLCPMCLIKRYYPVWIRSKTGQKIRFESVVDVALLYKNWRKIFDEKYGKDLVSKAREVSEDFVKDNMLVDSDLYYSSTWESGLSKKLKNKKEIDEEKVKEVVDFLNAAYKEIGNPPKYYAILVMDGDDMGKVISGEVLGEISTRIHPNIRDYVEIPEAKYYSTPQVHVAISQALANFSIREVRSVVKDEGLLIYAGGDDVLAILPVDKALEVAYKIRKEFGKSFENGSLLPGWKLSAGILIVHYKHPLYDALEKARDLLNNKAKNVPGKDTLAIGLLKRSGSYYISLVGWELIRVFYNSELRKKLLEEKGGVGKRFIYHVLREVDTWPKVGIDEMLKFEVIRHIRGRNKEETKELREKIYGEIKDLLEHVRGNNEVEKVRGLFTFLKIITDAEVFP 871
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhh.....hhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.eeeeeeee...eeehhhhhhhh...hhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhh......hhhhhhhhhhh..-----------.hhhhhhhhhhhhhhhhhhh....eeeeeeeee..----------------------------------.hhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeeeeehhhhhhhhhhhhhhhhhh..------...eeeeeeeee...hhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeeehhhhhhhhhhhhhhhhh..--.hhhhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGDEF  PDB: A:592-752 UniProt: 592-752                                                                                                                           ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w2v A 217 KDPTLLRIKIVPVQPFIANSRKQLDLWASSHLLSMLMYKALEVIVDKFGPEHVIYPSLRDQPFFLKFYLGENIGDEILVANLPNKALAIVSGKEAEKIEEEIKKRIRDFLLQLYREAVDWAVENGVVKVDRSEKDSMLKEAYLKIVREYFTVSITWVSLSEKEDIYQVTENAGLSDEDVKKWLKFAEKKENSRVLERIAIYPLLVKILDSLGERKVTEERFEKSEQLKGWKCHVCGENLAIFGDMYDHDNLKSLWLDEEPLCPMCLIKRYYPVWIRSKTGQKIRFESVVDVALLYKNWRKIFDEKYGKDLVSKAREVSEDFVKDNMLVDSDLYYSSTWESG-----------DEEKVKEVVDFLNAAYKEIGNPPKYYAILVMDGDD----------------------------------TPQVHVAISQALANFSIREVRSVVKDEGLLIYAGGDDVLAILPVDKALEVAYKIRKEFGKSFE------GWKLSAGILIVHYKHPLYDALEKARDLLNNKAKNVPGKDTLAIGLLKRSGSYYISLVGWELIRVFYNSELRKKLLEE--GVGKRFIYHVLREVDTWPKVGIDEMLKFEVIRHIRGRNKEETKELREKIYGEIKDLLEHVRGNNEVEKVRGLFTFLKIITDAEVFP 871
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556|        -  |    576       586       596      |  -         -         -         - |     646       656       666       676       686       696   |     -|      716       726       736       746       756       766       776      |786       796       806       816       826       836       846       856       866     
                                                                                                                                                                                                                                                                                                                                                                              557         569                               603                                638                                                           700    707                                                                         783  |                                                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   786                                                                                     


Chain B from PDB  Type:PROTEIN  Length:281
 aligned with CMR3_PYRFU | Q8U1S7 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:322
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  
           CMR3_PYRFU     1 MIEVTFTPYDVLLFRESRPFDAGSESVARSIIPLPQTVAGAIRTLLFYKGLKNCVGVGEEEPEFTLVGIAIGTEKGRIYPLPFNIIKSEKFYKVVNPGRFLGKLILPPKGKYKSGYVTESILEKYLKGELKEVEENKVIRIEKEKRIGIKLSREKKVVEEGMLYTVEFLRIEKIYAWIEDPGCGIKDILSSYEFLTLGGESRVAFVEVDDKTPDIFNRELGSTKKALFYFSTPTIGKVGEIVQELEKRLNAKIDDYLLVSSRPTAISGWDMHEKKPKGTKFAIPPGSVLFVEFKEEVEVPPYIKLGKLKKLGYGLALGGIWE 322
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.---------------------.hhhhhhhhhhhhhhhhh...............eeeeeeeee..eeeee....eeee..eeee...eee..eee..........eeehhhhhhhhh....eee.hhh....eeee.-----------------.eeee...eeeeeee....hhhhhhh...eee.---..eeeeeee...hhhhhh...eeeeeeeee...ee.hhhhhhhhhhhhhh..eeeeeee....eee.............eeee....eeeeeeeeeee...eee...hhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w2v B   1 MIEVTFTPYD---------------------IPLPQTVAGAIRTLLFYKGLKNCVGVGEEEPEFTLVGIAIGTEKGRIYPLPFNIIKSEKFYKVVNPGRFLGKLILPPKGKYKSGYVTESILEKYLKGELKEVEENKVIRIEKEKRI-----------------TVEFLRIEKIYAWIEDPGCGIKDILSSYEFLTL---SRVAFVEVDDKTPDIFNRELGSTKKALFYFSTPTIGKVGEIVQELEKRLNAKIDDYLLVSSRPTAISGWDMHEKKPKGTKFAIPPGSVLFVEFKEEVEVPPYIKLGKLKKLGYGLALGGIWE 322
                                    10         -         - |      40        50        60        70        80        90       100       110       120       130       140      |  -         -    |  170       180       190      |  -|      210       220       230       240       250       260       270       280       290       300       310       320  
                                    10                    32                                                                                                                147               165                             197 201
   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 3W2V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W2V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W2V)

(-) Gene Ontology  (5, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

Chain B   (CMR3_PYRFU | Q8U1S7)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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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  CMR2_PYRFU | Q8U1S6
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  CMR3_PYRFU | Q8U1S7
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 Related Entries

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

UniProtKB/Swiss-Prot
        CMR2_PYRFU | Q8U1S6: 3ung 3ur3 3w2w 3x1l 4doz 4h4k 4w8y
        CMR3_PYRFU | Q8U1S7: 3w2w 3x1l 4h4k

(-) Related Entries Specified in the PDB File

3w2w