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(-) Description

Title :  CRYSTAL STRUCTURE OF THE IMMATURE ENVELOPE GLYCOPROTEIN COMPLEX OF CHIKUNGUNYA VIRUS.
 
Authors :  J. Voss, M. C. Vaney, S. Duquerroy, F. A. Rey
Date :  21 May 10  (Deposition) - 01 Dec 10  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  F,P
Keywords :  Viral Protein, Immature Heterodimer, Alphavirus, Receptor Binding, Membrane Fusion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. E. Voss, M. C. Vaney, S. Duquerroy, C. Vonrhein, C. Girard-Blanc, E. Crublet, A. Thompson, G. Bricogne, F. A. Rey
Glycoprotein Organization Of Chikungunya Virus Particles Revealed By X-Ray Crystallography.
Nature V. 468 709 2010
PubMed-ID: 21124458  |  Reference-DOI: 10.1038/NATURE09555
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P62 ENVELOPE GLYCOPROTEIN
    ChainsP
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System Cell LineSCHNEIDER 2
    Expression System PlasmidPMRBIP/V5 HISA
    Expression System Taxid7227
    Expression System Vector TypePLASMID
    FragmentPOLYPROTEIN FRAGMENT RESIDUES 266-666
    MutationYES
    Organism CommonCHIKV
    Organism ScientificCHIKUNGUNYA VIRUS
    Organism Taxid37124
    Strain05-115
 
Molecule 2 - E1 ENVELOPE GLYCOPROTEIN
    ChainsF
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System Cell LineSCHNEIDER 2
    Expression System PlasmidPMRBIP/V5 HISA
    Expression System Taxid7227
    Expression System Vector TypePLASMID
    FragmentPOLYPROTEIN FRAGMENT RESIDUES 810-1200
    Organism CommonCHIKV
    Organism ScientificCHIKUNGUNYA VIRUS
    Organism Taxid37124
    Strain05-115

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit FP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER F:167 , ASN P:12 , ASN P:282 , ASN P:283 , NAG P:1002BINDING SITE FOR RESIDUE NAG P 1001
02AC2SOFTWAREASN P:283 , NAG P:1001BINDING SITE FOR RESIDUE NAG P 1002
03AC3SOFTWAREASN P:327BINDING SITE FOR RESIDUE NAG P 2001
04AC4SOFTWAREPHE P:70 , VAL P:72 , TYR P:73 , HIS P:126BINDING SITE FOR RESIDUE ACT P 1
05AC5SOFTWAREARG P:144 , ILE P:157 , THR P:158 , GLY P:159 , THR P:160 , HOH P:467BINDING SITE FOR RESIDUE ACT P 2
06AC6SOFTWAREHIS P:126 , TRP P:128 , HOH P:516BINDING SITE FOR RESIDUE ACT P 3
07AC7SOFTWARETHR P:66 , ASP P:68 , ASN P:69BINDING SITE FOR RESIDUE ACT P 406
08AC8SOFTWAREARG F:134 , GLY F:139 , ASN F:141 , HOH F:395 , NDG F:1002BINDING SITE FOR RESIDUE NAG F 1001
09AC9SOFTWARENAG F:1001BINDING SITE FOR RESIDUE NDG F 1002
10BC1SOFTWARESER F:77 , LEU F:219 , VAL F:220 , LEU F:221BINDING SITE FOR RESIDUE ACT F 392

(-) SS Bonds  (17, 17)

Asymmetric/Biological Unit
No.Residues
1F:49 -F:114
2F:62 -F:94
3F:63 -F:96
4F:68 -F:78
5F:259 -F:271
6F:301 -F:376
7F:306 -F:380
8F:328 -F:370
9P:8 -P:17
10P:22 -P:26
11P:25 -P:57
12P:83 -P:189
13P:86 -P:92
14P:155 -P:169
15P:217 -P:330
16P:265 -P:289
17P:267 -P:284

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr P:23 -Pro P:24
2Gly F:164 -Pro F:165
3Asn F:264 -Pro F:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N40)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N40)

(-) Exons   (0, 0)

(no "Exon" information available for 3N40)

(-) 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 F from PDB  Type:PROTEIN  Length:393
 aligned with Q1H8W5_CHIKV | Q1H8W5 from UniProtKB/TrEMBL  Length:1248

    Alignment length:393
                                   817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197   
        Q1H8W5_CHIKV    808 SAYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYP 1200
               SCOP domains d3n40f1 F:-1-292 automated matches                                                                                                                                                                                                                                                                    d3n40f2 F:293-391 automated matches                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Alpha_E1_glycop-3n40F01 F:1-391                                                                                                                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author ..eeeeeeee......eeeee.......eeeeeeeeeeeeeeeeeeeeee..eeee....eee...............eeeeee....ee..ee........eeeeeeeeee.hhhhh..eeeeeeeeeeeeeeeeeee..eeeeeeee.....eeee..eeeee............eeeee..eeee................ee.........ee....ee...........ee...hhhhhhhhhh..hhhhhhhhhheee....eee.....eeeeeeeehhhhh........eeeeeeeeeee.......eeeeeeeee...eeeeeee....eee...eeee..eeeeeeeeee...eeeeeeee..eeeeeeee.......ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3n40 F   -1 GGYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYP  391
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388   

Chain P from PDB  Type:PROTEIN  Length:401
 aligned with Q1H8W5_CHIKV | Q1H8W5 from UniProtKB/TrEMBL  Length:1248

    Alignment length:401
                                   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 
        Q1H8W5_CHIKV    266 PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSPHRQRRSTKDNFNVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQ  666
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Alpha_E3_glycop-3n40P02 P:7-65                             ------------Alpha_E2_glycop-3n40P01 P:78-405                                                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author ..eeee..eeee................................................................eee........eee...eeeee.......eeeeeeeeeee.....eeeeeeeeee..eeeeee....eee.....eeeeeeeeeeeee...eeeeeeeee.....eeeeeeeeee.................eeeeeeee.........eeeee....ee....eeee..eeee......eeeee......eeee...eee.......eeeee......ee...............eeee....eeeeeeee......eeeee..eeeeee.....eeeeeee.......eeeee...eeeeee.....eeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3n40 P    5 PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSPHRQRESTKDNFNVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQ  405
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404 

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N40)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain F,P   (Q1H8W5_CHIKV | Q1H8W5)
molecular function
    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: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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q1H8W5_CHIKV | Q1H8W52xfb 2xfc 3j2w 3n41 3n42 3n43 3n44 5any

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3N40)