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(-) Description

Title :  CRYSTAL STRUCTURE OF MACRO DOMAIN OF CHIKUNGUNYA VIRUS IN COMPLEX WITH RNA
 
Authors :  H. Malet, S. Jamal, B. Coutard, B. Canard
Date :  23 Mar 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Macro Domain, X Domain, Chikungunya, Alphavirus, Virus, Vizier. Viral Enzymes Involved In Replication, Rna, Atp-Binding, Cell Membrane, Endosome, Helicase, Hydrolase, Lipoprotein, Lysosome, Membrane, Methyltransferase, Mrna Capping, Mrna Processing, Multifunctional Enzyme, Nucleotide-Binding, Nucleotidyltransferase, Nucleus, Palmitate, Phosphoprotein, Protease, Rna Replication, Rna-Binding, Rna-Directed Rna Polymerase, Thiol Protease, Transferase, Viral Protein/Rna, Viral Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Malet, B. Coutard, S. Jamal, H. Dutartre, N. Papageorgiou, M. Neuvonen, T. Ahola, N. Forrester, E. A. Gould, D. Lafitte, F. Ferron J. Lescar, A. E. Gorbalenya, X. De Lamballerie, B. Canard
The Crystal Structures Of Chikungunya And Venezuelan Equine Encephalitis Virus Nsp3 Macro Domains Define A Conserved Adenosine Binding Pocket
J. Virol. V. 83 6534 2009
PubMed-ID: 19386706  |  Reference-DOI: 10.1128/JVI.00189-09

(-) Compounds

Molecule 1 - NON-STRUCTURAL PROTEIN 3
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST14
    Expression System StrainROSETTA (DE3) PLYSS
    Expression System Taxid562
    Expression System VectorGATEWAY
    FragmentSEQUENCE DATABASE RESIDUES 1334-1493
    GeneNSP3
    Organism ScientificCHIKUNGUNYA VIRUS
    Organism Taxid371094
    StrainROSS
    SynonymNSP3
 
Molecule 2 - RNA (5'-R(*AP*AP*A)-3')
    ChainsE, F
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A   E 
Biological Unit 2 (1x) B   F
Biological Unit 3 (1x)  C   
Biological Unit 4 (1x)   D  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3GPQ)

(-) Sites  (0, 0)

(no "Site" information available for 3GPQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GPQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GPQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3GPQ)

(-) Sequences/Alignments

Asymmetric 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:160
 aligned with POLN_CHIKS | Q8JUX6 from UniProtKB/Swiss-Prot  Length:2474

    Alignment length:160
                                  1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483      1493
          POLN_CHIKS   1334 APSYRVKRMDIAKNDEECVVNAANPRGLPGDGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKISEAIQMRT 1493
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhh....eeee........hhhhhhhhhhhhhhhh........eeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh....hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gpq A    1 APSYRVKRMDIAKNDEECVVNAANPRGLPGDGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKISEAIQMRT  160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with POLN_CHIKS | Q8JUX6 from UniProtKB/Swiss-Prot  Length:2474

    Alignment length:160
                                  1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483      1493
          POLN_CHIKS   1334 APSYRVKRMDIAKNDEECVVNAANPRGLPGDGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKISEAIQMRT 1493
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhh....eeee.........hhhhhhhhhhhhhhh........eeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh....hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gpq B    1 APSYRVKRMDIAKNDEECVVNAANPRGLPGDGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKISEAIQMRT  160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:150
 aligned with POLN_CHIKS | Q8JUX6 from UniProtKB/Swiss-Prot  Length:2474

    Alignment length:159
                                  1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483         
          POLN_CHIKS   1334 APSYRVKRMDIAKNDEECVVNAANPRGLPGDGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKISEAIQMR 1492
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhh....eeee...-..-----.hhhhhhhhhhhh.........--.ee..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh...-.ee............hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gpq C    1 APSYRVKRMDIAKNDEECVVNAANP-GL-----CKAVYKKWPESFKNSATPVGTA--VMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNS-AIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKISEAIQMR  159
                                    10        20    | || -   |    40        50    |  |60        70        80        90       100  | |  110       120       130       140       150         
                                                   25 ||    34                   55 58                                          103 |                                                      
                                                     27|                                                                          105                                                      
                                                      28                                                                                                                                   

Chain D from PDB  Type:PROTEIN  Length:148
 aligned with POLN_CHIKS | Q8JUX6 from UniProtKB/Swiss-Prot  Length:2474

    Alignment length:152
                                  1344      1354      1364      1374      1384      1394      1404      1414      1424      1434      1444      1454      1464      1474      1484  
          POLN_CHIKS   1335 PSYRVKRMDIAKNDEECVVNAANPRGLPGDGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDSTDADVVIYCRDKEWEKKIS 1486
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhh....eeee........hhhhhhhhhhhhhhhh........eeeeee..eeeeee.......-..-hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhh....hhhhhhhhhhhhhh..--.eeeee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gpq D    2 PSYRVKRMDIAKNDEECVVNAANPRGLPGDGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAVGPNFSN-SE-EGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHLFTAMDST--DVVIYCRDKEWEKKIS  153
                                    11        21        31        41        51        61        71   | || 81        91       101       111       121       131   |  |141       151  
                                                                                                    75 || |                                                    135  |               
                                                                                                      77| |                                                       138               
                                                                                                       78 |                                                                         
                                                                                                         80                                                                         

Chain E from PDB  Type:RNA  Length:2
                                   
                3gpq E    1 AA    2

Chain F from PDB  Type:RNA  Length:2
                                   
                3gpq F    1 AA    2

   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 3GPQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 39)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (POLN_CHIKS | Q8JUX6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008174    mRNA methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an mRNA molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    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.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004651    polynucleotide 5'-phosphatase activity    Catalysis of the reaction: 5'-phosphopolynucleotide + H2O = polynucleotide + phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0080009    mRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0098507    polynucleotide 5' dephosphorylation    The process of removing one or more phosphate groups from the 5' end of a polynucleotide.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039523    suppression by virus of host RNA polymerase II activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host RNA polymerase II activity.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    GO:0044188    host cell lysosomal membrane    The lipid bilayer surrounding the host cell lysosome and separating its contents from the host cell cytoplasm.
    GO:0044187    host cell lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most host animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and host cell lysosomes have a great variety of morphologies and functions.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POLN_CHIKS | Q8JUX63gpg 3gpo 3trk 4tu0 5i22

(-) Related Entries Specified in the PDB File

3gpg CRYSTAL STRUCTURE OF CHIKUNGUNYA MACRO DOMAIN
3gpo CRYSTAL STRUCTURE OF CHIKUNGUNYA MACRO DOMAIN IN COMPLEX WITH ADP-RIBOSE
3gqe