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(-) Description

Title :  EQUINE RHINITIS A VIRUS IN COMPLEX WITH ITS SIALIC ACID RECEPTOR
 
Authors :  E. E. Fry, T. J. Tuthill, K. Harlos, T. S. Walter, D. J. Rowlands, D. I. Stu
Date :  14 Apr 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym. Unit :  1,2,3,4
Biol. Unit 1:  1,2,3,4  (60x)
Keywords :  Virus, Capsid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. E. Fry, T. J. Tuthill, K. Harlos, T. S. Walter, D. J. Rowlands, D. I. Stuart
The Crystal Structure Of Equine Rhinitis A Virus In Complex With Its Sialic Acid Receptor.
J. Gen. Virol. V. 91 1971 2010
PubMed-ID: 20427563  |  Reference-DOI: 10.1099/VIR.0.020420-0

(-) Compounds

Molecule 1 - P1
    Chains: 1
    Fragment: CAPSID PROTEIN VP1, RESIDUES 537-784
    Organism Scientific: EQUINE RHINITIS A VIRUS
    Organism Taxid: 47000
    Strain: NM11/67
 
Molecule 2 - P1
    Chains: 2
    Fragment: CAPSID PROTEIN VP2, RESIDUES 81-310
    Organism Scientific: EQUINE RHINITIS A VIRUS
    Organism Taxid: 47000
    Strain: NM11/67
 
Molecule 3 - P1
    Chains: 3
    Fragment: CAPSID PROTEIN VP3, RESIDUES 311-536
    Organism Scientific: EQUINE RHINITIS A VIRUS
    Organism Taxid: 47000
    Strain: NM11/67
 
Molecule 4 - P1
    Chains: 4
    Fragment: CAPSID PROTEIN VP4, RESIDUES 1-80
    Organism Scientific: EQUINE RHINITIS A VIRUS
    Organism Taxid: 47000
    Strain: NM11/67

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : 1234
Biological Unit 1 (60x): 1234

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GLC1Ligand/IonALPHA-D-GLUCOSE
3SIA1Ligand/IonO-SIALIC ACID
Biological Unit 1 (3, 180)
No.NameCountTypeFull Name
1GAL60Ligand/IonBETA-D-GALACTOSE
2GLC60Ligand/IonALPHA-D-GLUCOSE
3SIA60Ligand/IonO-SIALIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN 1:65BINDING SITE FOR CHAIN 1 OF POLYSACCHARIDE RESIDUES 1247 TO 1249

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XBO)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu 2:83 -Pro 2:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XBO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XBO)

(-) Exons   (0, 0)

(no "Exon" information available for 2XBO)

(-) 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 1 from PDB  Type:PROTEIN  Length:247
 aligned with B9VV85_9PICO | B9VV85 from UniProtKB/TrEMBL  Length:784

    Alignment length:247
                                   546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       
         B9VV85_9PICO   537 VTNVGEDGEPGETEPRHALSPVDMHVHTDVSFLLDRFFDVETLELSNLTGSPATHVLDPFGSTAQLAWARLLNTCTYFFSDLELSIQFKFTTTPSSVGEGFVWVKWFPVGAPTKTTDAWQLEGGGNSVRIQQLAVAGMSPTVVFKIAGSRSQACGFSVPYTSMWRVVPVFYNGWGAPTKEKATYNWLPGAHFGSILLTSDAHDKGGCYLRYRFPRANMYCPRPIPPAFTRPADKTRHKFPTNINKQC 783
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhhhh..ee...............ee..................eeeee..eeeee..ee..hhhhh...eeeeeee.........eeee........eee.........eeeee........eeeee........ee.........................eeeeee.....ee..eeee....eeeee.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xbo 1   1 VTNVGEDGEPGETEPRHALSPVDMHVHTDVSFLLDRFFDVETLELSNLTGSPATHVLDPFGSTAQLAWARLLNTCTYFFSDLELSIQFKFTTTPSSVGEGFVWVKWFPVGAPTKTTDAWQLEGGGNSVRIQQLAVAGMSPTVVFKIAGSRSQACGFSVPYTSMWRVVPVFYNGWGAPTKEKATYNWLPGAHFGSILLTSDAHDKGGCYLRYRFPRANMYCPRPIPPAFTRPADKTRHKFPTNINKQC 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       


Chain 2 from PDB  Type:PROTEIN  Length:200
 aligned with B9VV85_9PICO | B9VV85 from UniProtKB/TrEMBL  Length:784

    Alignment length:200
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
         B9VV85_9PICO   111 GTTYCYSKPDGRPPSTVSDPVTRLGPTLSRHYTFKVGEWPHSQSHGHAWICPLPGDKLKKMGSFHEVVKAHHLVKNGWDVVVQVNASFAHSGALCVAAVPEYEHTHEKALKWSELEEPAYTYQQLSVFPHQLLNLRTNSSVHLVMPYIGPGPTTNLTLHNPWTIVILILSELTGPGQTVPVTMSVAPIDAMVNGPLPNPE 310
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.................eee.......eeeeeeee.......eeeeee...hhhhhh.hhhhhhhh..eeeeeeeeee..........eeeeeeee...hhhhh....eeee..hhhhhhhh...eeeee......eeeee................eeeeeeeee........eeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xbo 2  31 GTTYCYSKPDGRPPSTVSDPVTRLGPTLSRHYTFKVGEWPHSQSHGHAWICPLPSDKLKKMGSFHEVVKAHHLVKNGWDVVVQVNASFAHSGALCVAAVPEYEHTHEKALKWSELEEPAYTYQQLSVFPHQLLNLRTNSSVHLVMPYIGPGPTTNLTLHNPWTIVILILSELTGPGQTVPVTMSVAPIDAMVNGPLPNPE 230
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230


Chain 3 from PDB  Type:PROTEIN  Length:226
 aligned with B9VV85_9PICO | B9VV85 from UniProtKB/TrEMBL  Length:784

    Alignment length:226
                                   320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530      
         B9VV85_9PICO   311 APIRVVSVPESDSFMSSVPDNSTPLYPKVVVPPRQVPGRFTNFIDVAKQTYSFCSISGRPYFEVTNTSGDEPLFQMDVSLSAAELHGTYVASLSSFFAQYRGSLNFNFIFTGAAATKAKFLVAFVPPHSAAPKTRDEAMACIHAVWDVGLNSAFSFNVPYSSPADFMAVYSAEATVVNVSGWLQVYALTALTSTDIAVNSKGRVLVAVSAGPDFSLRHPVDLPDKQ 536
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2xbo300 3:1-226  [code=2.60.120.20, no name defined]                                                                                                                                                                               CATH domains
           Pfam domains (1) -----------------------------Rhv-2xbo301 3:30-187                                                                                                                                          --------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------Rhv-2xbo302 3:30-187                                                                                                                                          --------------------------------------- Pfam domains (2)
         Sec.struct. author ............................ee........ee.hhhhhhhh..ee.......eeeee........eeeee....hhhh.hhhhhhhh...eee..eeeeeee.....eeeeeeeeee........hhhhhh..eeeeeee....eeeeee........ee............eeeeeee....ee.......eeeeeeeeee....eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xbo 3   1 APIRVVSVPESDSFMSSVPDNSTPLYPKVVVPPRQVPGRFTNFIDVAKQTYSFCSISGKPYFEVTNTSGDEPLFQMDVSLSAAELHGTYVASLSSFFAQYRGSLNFYFIFTGAAATKAKFLVAFVPPHSAAPKTRDEAMACIHAVWDVGLNSAFSFNVPYSSPADFMAVYSAEATVVNVSGWLQVYALTALTSTDIAVNSKGRVLVAVSAGPDFSLRHPVDLPDKQ 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      


Chain 4 from PDB  Type:PROTEIN  Length:22
 aligned with B9VV85_9PICO | B9VV85 from UniProtKB/TrEMBL  Length:784

    Alignment length:22
                                    25        35  
         B9VV85_9PICO    16 GNSGSIVQNFYMQQYQNSIDAD  37
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains VP4_2-2xbo401 4:16-37  Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhee... Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 2xbo 4  16 GNSGSIVQNFYMQQYQNSIDAD  37
                                    25        35
   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 2XBO)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 3)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)
(-)
Family: Rhv (55)
(-)
Clan: no clan defined [family: VP4_2] (10)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain 1,2,3,4   (B9VV85_9PICO | B9VV85)
molecular function
    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.
cellular component
    GO:0019030    icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form an icosahedron, a solid with 20 faces and 12 vertices. Icosahedral capsids have 12 pentamers plus 10(T-1) hexamers, where T is the triangulation number. Tobacco satellite necrosis virus has such a capsid structure.
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        B9VV85_9PICO | B9VV85: 2wff 2ws9 4ctg

(-) Related Entries Specified in the PDB File

2wff EQUINE RHINITIS A VIRUS
2ws9 EQUINE RHINITIS A VIRUS AT LOW PH