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(-) Description

Title :  CRYSTAL STRUCTURE OF MAJOR CAPSID PROTEIN P DOMAIN FROM RABBIT HEMORRHAGIC DISEASE VIRUS
 
Authors :  X. Wang, F. Xu, K. Zhang, Y. Zhai, F. Sun
Date :  01 Apr 12  (Deposition) - 30 Jan 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Protein, Capsid Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Wang, F. Xu, J. Liu, B. Gao, Y. Liu, Y. Zhai, J. Ma, K. Zhang, T. S. Baker K. Schulten, D. Zheng, H. Pang, F. Sun
Atomic Model Of Rabbit Hemorrhagic Disease Virus By Cryo-Electron Microscopy And Crystallography.
Plos Pathog. V. 9 03132 2013
PubMed-ID: 23341770  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003132

(-) Compounds

Molecule 1 - MAJOR CAPSID PROTEIN VP60
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTEL-3G
    Expression System Strain: SF21
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: P (PROTRUDING) DOMAIN (UNP RESIDUES 228-579)
    Gene: VP60
    Organism Common: RHDV
    Organism Scientific: RABBIT HEMORRHAGIC DISEASE VIRUS
    Organism Taxid: 11976

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4EGT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:346 -Pro A:347
2Ala A:384 -Pro A:385
3Asn A:414 -Pro A:415
4Thr A:437 -Pro A:438
5Ser B:346 -Pro B:347
6Ala B:384 -Pro B:385
7Asn B:414 -Pro B:415
8Thr B:437 -Pro B:438

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EGT)

(-) 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 A from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..........eeeeeee....ee......................eeeeeeeeeee.......eeeeeee.................................eeeeeeeee.......hhhhheeeeeeeee......ee.......eeeeee.........eeeeeeee....eee........ee.hhhhh.......ee......eeeeeeee..ee...eeee..hhhhhhhhhhh.........eeeeeeeee...eeeeee.....eee........ee...eeeeeeeeeee......ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4egt A 238 SPAGLLTTPVLTGVGNDNRWNGQIVRLQPVPGGFSTCNRHWNLNGSTYGWSSPRFADIDHRRGSASYSGNSSTNVLQFWYANAGSAIDNPISQVAPDGFPDMSFVPFNSPNIPTAGWVGFGGIWNSNNGAPAATTVQAYELGFATGAPNNLQPTTNTSGAQTVAKSIYAVVTGTNQNPTGLFVMASGVISTPNASAVTYTPQPDRIVTTPGTPAAAPVGKNTPIMFASVVRRTGTQYGTGSQPLPVTIGLSLNNYSSALMPGQFFVWQLTFASGFMEIGLSVDGYFYAGTEASTTLIDLTELIDVRPVGPRPSKSTLVFNLGFSYV 579
                                   247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467   ||  488       498       508       518       528       538       548       558       568||    
                                                                                                                                                                                                                                                                   471|                                                                                   569|    
                                                                                                                                                                                                                                                                    483                                                                                    575    


Chain B from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..........eeeeeee....ee.....................eeeeeeeeee......eee..eeeee.................................eeeeeeeee.......hhhhheeeeeeeee......ee.......eeeeee...eee......eeeeee...eee.......ee.hhhhh.......ee......eeeeeeee..ee........eeee..hhhhhhhhhhh.........eeeeeeeee...eeeeee.....eee........ee...eeeeeeeeeee......ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4egt B 238 SPAGLLTTPVLTGVGNDNRWNGQIVRLQPVPGGFSTCNRHWNLNGSTYGWSSPRFADIDHRRGSASYSGNSSTNVLQFWYANAGSAIDNPISQVAPDGFPDMSFVPFNSPNIPTAGWVGFGGIWNSNNGAPAATTVQAYELGFATGAPNNLQPTTNTSGAQTVAKSIYAVVTGTNQNPTGLFVMASGVISTPNASATYTPQPDRIVTTPGTPAAAPVGKNTPIMFASVVRRTGDVNAAAQYGTGSQPLPVTIGLSLNNYSSALMPGQFFVWQLTFASGFMEIGLSVDGYFYAGTEASTTLIDLTELIDVRPVGPRPSKSTLVFNLGGFSYV 579
                                   247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427     ||438       448       458       468       484       494       504       514       524       534       544       554       564     ||578 
                                                                                                                                                                                                                             433|                                       477|                                                                                   570|    
                                                                                                                                                                                                                              435                                        484                                                                                    575
   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 4EGT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 4egt)
 
  Cis Peptide Bonds
    Ala A:384 - Pro A:385   [ RasMol ]  
    Ala B:384 - Pro B:385   [ RasMol ]  
    Asn A:414 - Pro A:415   [ RasMol ]  
    Asn B:414 - Pro B:415   [ RasMol ]  
    Ser A:346 - Pro A:347   [ RasMol ]  
    Ser B:346 - Pro B:347   [ RasMol ]  
    Thr A:437 - Pro A:438   [ RasMol ]  
    Thr B:437 - Pro B:438   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q3HNQ1_RHDV | Q3HNQ1: 4ejr
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(-) Related Entries Specified in the PDB File

4ejr CRYSTAL STRUCTURE OF S DOMAIN OF MAJOR CAPSID PROTEIN VP60 FROM RABBIT HEMORRHAGIC DISEASE VIRUS
4j1p ATOMIC MODEL OF RABBIT HEMORRHAGIC DISEASE VIRUS