Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  HUMAN ENTEROVIRUS 71 UNCOATING INTERMEDIATE CAPTURED AT ATOMIC RESOLUTION
 
Authors :  R. Chen, K. Lyu
Date :  08 Oct 13  (Deposition) - 05 Feb 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Hand-Foot-And-Mouth Disease, Picornavirus, Human Enterovirus 71, Uncoating Intermediate, Icosahedral Virus, Pocket Factor, 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
    Fragment: EV71 CAPSID PROTEIN VP1
    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
    Fragment: EV71 CAPSID PROTEIN VP2
    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
    Fragment: EV71 CAPSID PROTEIN VP3
    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

  123
Asymmetric Unit : ABC
Biological Unit 1 (60x): ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4N43)

(-) Sites  (0, 0)

(no "Site" information available for 4N43)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N43)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe B:82 -Pro B:83
2Ile C:235 -Leu C:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N43)

(-) Exons   (0, 0)

(no "Exon" information available for 4N43)

(-) 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:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh..eeeeeeee..........eeeee.hhhhhhhhhhhhh...eeeeeeeeeeeee.........eeeeeee.....................eeeee.....eeeee........ee.............................eeeeee.........eeeeeeeeeeeeee.................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n43 A  72 SHSTAETTLDSFFSRAGLVGEIDLPLEGTTNPNGYANWDIDITGYAQMRRKVELFTYMRFDAEFTFVACTPTGEVVPQLLQYMFVPPGAPKPDSRESLAWQTATNPSVFVKLSDPPAQVSVPFMSPASAYQWFYDGYPTFGEHKQEKDLEYGACPNNMMGTFSVRTVGTSKSKYPLVVRIYMRMKHVRAWIPRPMRNQNYLFKANPNYAGNSIKPTGASRTAITT 296
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     


Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee.........ee........................eeeeeeee......eeeeehhhhh..hhhhhhhh........eeeeeee........eeeeeeee..................hhhhhh.....ee..hhhhh....hhhhhhhh.eeeee.....eeeeee................eeeeeeeee...........eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n43 B  16 LTIGNSTITTQEAANIIVGYGEWPSYCSDSDATRPDVSVNRFYTLDTKLWEKSSKGWYWKFPDVLTETGVFGQNAQFHYLYRSGFCIHVQCNASKFHQGALLVAVLPEYVIGTVAGGTGTEDSHPPYKQTQPGADGFELQHPYVLDAGIPISQLTVCPHQWINLRTNNCATIIVPYINALPFDSALNHCNFGLLVVPISPLDYDQGATPVIPITITLAPMCSEFAGLRQ 250
                                    25        35        45 ||     61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
                                                          47|                                                                                                                                                                                                    
                                                           54                                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................................hhhhhh..eee..........hhhhh.eeeee........eeeee......hhhhhhhhhhhhh....eeeeeeeeeee........eeeeeee........hhhhhhh..eeeee.......eeeeeee.......eeeeee............eeeeeeeeee....ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n43 C   1 GFPTELKPGTNQFLTTDDGVSAPILPNFHPTPCIHIPGEVRNLLELCQVETILEVNNVPTNATSLMERLRFPVSAQAGKGELCAVFRADPGRSGPWQSTLLGQLCGYYTQWSGSLEVTFMFTGSFMATGKMLIAYTPPGGPLPKDRATAMLGTHVIWDFGLQSSVTLVIPWISNTYTTGLVSIWYQTNYVVPIGAPNTAYIIALAAAQKNFTMQLCKDASDIL 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    || 193       203       213       223       233   
                                                                                                                                                                                                        175|                                               
                                                                                                                                                                                                         189
   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 4N43)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N43)

(-) Gene Ontology  (36, 108)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4n43)
 
  Sites
(no "Sites" information available for 4n43)
 
  Cis Peptide Bonds
    Ile C:235 - Leu C:236   [ RasMol ]  
    Phe B:82 - Pro B:83   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4n43
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  M9XM90_9ENTO | M9XM90
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q9WPJ0_9ENTO | Q9WPJ0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q9WQJ0_9ENTO | Q9WQJ0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  M9XM90_9ENTO | M9XM90
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9WPJ0_9ENTO | Q9WPJ0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9WQJ0_9ENTO | Q9WQJ0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4N43)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4N43)