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(-) Description

Title :  HUMAN ENTEROVIRUS 71 UNCOATING INTERMEDIATE CAPTURED AT ATOMIC RESOLUTION
 
Authors :  R. Chen, K. Lyu
Date :  09 Oct 13  (Deposition) - 05 Feb 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.31
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Hand-Foot-And-Mouth Disease, Human Enterovirus 71, Virion, Pocket Factor, Picornavirus, Icosahedral Virus, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Lyu, J. Ding, J. F. Han, Y. Zhang, X. Y. Wu, Y. L. He, C. F. Qin, R. Chen
Human Enterovirus 71 Uncoating Captured At Atomic Resolution.
J. Virol. V. 88 3114 2014
PubMed-ID: 24352461  |  Reference-DOI: 10.1128/JVI.03029-13

(-) Compounds

Molecule 1 - CAPSID PROTEIN VP1
    Chains: A
    Organism Scientific: ENTEROVIRUS A71
    Organism Taxid: 39054
    Other Details: ISOLATED IN FUYANG, ANHUI IN 2008, GROW IN RD CELLS
    Strain: CLINICAL C4 STRAIN, AH08/06, GENBANK ACCESSION NO. HQ611148
 
Molecule 2 - CAPSID PROTEIN VP2
    Chains: B
    Organism Scientific: ENTEROVIRUS A71
    Organism Taxid: 39054
    Other Details: ISOLATED IN FUYANG, ANHUI IN 2008, GROW IN RD CELLS
    Strain: CLINICAL C4 STRAIN, AH08/06, GENBANK ACCESSION NO. HQ611148
 
Molecule 3 - CAPSID PROTEIN VP3
    Chains: C
    Organism Scientific: ENTEROVIRUS A71
    Organism Taxid: 39054
    Other Details: ISOLATED IN FUYANG, ANHUI IN 2008, GROW IN RD CELLS
    Strain: CLINICAL C4 STRAIN, AH08/06, GENBANK ACCESSION NO. HQ611148
 
Molecule 4 - CAPSID PROTEIN VP4
    Chains: D
    Organism Scientific: ENTEROVIRUS A71
    Organism Taxid: 39054
    Other Details: ISOLATED IN FUYANG, ANHUI IN 2008, GROW IN RD CELLS
    Strain: CLINICAL C4 STRAIN, AH08/06, GENBANK ACCESSION NO. HQ611148

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SPH1Ligand/IonSPHINGOSINE
Biological Unit 1 (1, 60)
No.NameCountTypeFull Name
1SPH60Ligand/IonSPHINGOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:111 , ASP A:112 , ILE A:113 , THR A:114 , PHE A:135 , PHE A:155 , MET A:195 , TRP A:203 , ASN A:228 , ALA A:275BINDING SITE FOR RESIDUE SPH A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N53)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asp A:2 -Arg A:3
2Thr A:237 -Val A:238
3Gly A:239 -Thr A:240
4Phe B:82 -Pro B:83
5Thr C:60 -Asn C:61
6Ser C:93 -Gly C:94
7Arg C:182 -Asp C:183
8Thr C:238 -Gly C:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N53)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N53)

(-) Exons   (0, 0)

(no "Exon" information available for 4N53)

(-) 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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..............ee.....................eehhhhh.....hhhhh...........hhhhhhhhhhh..eeeeeeee...........eeee.....hhhhhhhhh...eeeeeeeeeeeee.........eeeeeee...........hhhhhh....eeeee.....eeeee........ee......................hhhhh..eeee...........eeeeeeeeeeeeee..................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n53 A   1 GDRVADVIESSIGDSVSRALTHALPAPTGQNTQVSSHRLDTGKVPALQAAEIGASSNASDESMIETRCVLNSHSTAETTLDSFFSRAGLVGEIDLPLEGTTNPNGYANWDIDITGYAQMRRKVELFTYMRFDAEFTFVACTPTGEVVPQLLQYMFVPPGAPKPDSRESLAWQTATNPSVFVKLSDPPAQVSVPFMSPASAYQWFYDGYPTFGEHKQEKDLEYGACPNNMMGTFSVRTVGTSKSKYPLVVRIYMRMKHVRAWIPRPMRNQNYLFKANPNYAGNSIKPTGASRTAITTL 297
                                    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       


Chain B from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..eeeee..............................hhhhh...eeeeeee.......eeeee......hhhhhhhhhheeeeeeeeee..........eeeeeeeeee..................hhhhhh.....ee...........hhhhh....eeeee........eee................eeeeeeeeeeee.........eeeeee.eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4n53 B   9 YSDRVAQLTIGNSTITTQEAANIIVGYGEWPSYCSDSDATAVDKPTRPDVSVNRFYTLDTKLWEKSSKGWYWKFPDVLTETGVFGQNAQFHYLYRSGFCIHVQCNASKFHQGALLVAVLPEYVIGTVAGGTGTEDSHPPYKQTQPGADGFELQHPYVLDAGIPISQLTVCPHQWINLRTNNCATIIVPYINALPFDSALNHCNFGLLVVPISPLDYDQGATPVIPITITLAPMCSEFAGLRQAVTQ 254
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248      


Chain C from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................ee...................hhhhhh..ee..........hhhhhhhheeee.......eeeeee......hhhhhhhhhhhhh...eee..eeeeeee........eeeeeee........hhhhh...eeeeee.....eeeeee........ee....hhhhhhh..eeeeee............eeeeeeeeee....ee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n53 C   1 GFPTELKPGTNQFLTTDDGVSAPILPNFHPTPCIHIPGEVRNLLELCQVETILEVNNVPTNATSLMERLRFPVSAQAGKGELCAVFRADPGRSGPWQSTLLGQLCGYYTQWSGSLEVTFMFTGSFMATGKMLIAYTPPGGPLPKDRATAMLGTHVIWDFGLQSSVTLVIPWISNTHYRAHARDGVFDYYTTGLVSIWYQTNYVVPIGAPNTAYIIALAAAQKNFTMQLCKDASDILQTGTIQ 242
                                    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 D from PDB  Type:PROTEIN  Length:58
                                                                                          
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhh.......ee.hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 4n53 D  12 SHENSNSATEGSTINYTTINYYKDSYAATAGKQSLKQDPDKFANPVKDIFTEMAAPLK  69
                                    21        31        41        51        61
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4N53)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N53)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N53)

(-) Gene Ontology  (36, 78)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4n43