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(-) Description

Title :  CRYSTAL STRUCTURE OF ACMNPV BACULOVIRUS POLYHEDRA
 
Authors :  F. Coulibaly, E. Chiu, P. Metcalf
Date :  17 Sep 09  (Deposition) - 08 Dec 09  (Release) - 12 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Jelly-Roll, Disulfide Bond, Domain Swapping, Viral Occlusion Body, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Coulibaly, E. Chiu, S. Gutmann, C. Rajendran, P. W. Haebel, K. Ikeda, H. Mori, V. K. Ward, C. Schulze-Briese, P. Metcalf
The Atomic Structure Of Baculovirus Polyhedra Reveals The Independent Emergence Of Infectious Crystals In Dna And Rna Viruses
Proc. Natl. Acad. Sci. Usa V. 106 22205 2009
PubMed-ID: 20007786  |  Reference-DOI: 10.1073/PNAS.0910686106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYHEDRIN
    Cell: SF21
    Chains: A
    Mutation: YES
    Organism Common: ACMNPV
    Organism Scientific: AUTOGRAPHA CALIFORNICA NUCLEOPOLYHEDROVIRUS
    Organism Taxid: 46015
    Other Details: CRYSTALS WERE PURIFIED FROM SF21 CELLS INFECTED BY THE AUTOGRAPHA CALIFORNICA MULTICAPSID NUCLEOPOLYHEDROVIRUS (ACMNPV)
    Synonym: MAJOR OCCLUSION PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 60)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2MSE48Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:154 , VAL A:156 , GLU A:232 , HOH A:284BINDING SITE FOR RESIDUE EDO A 246

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:132 -A:132

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:107 -Pro A:108
2Gly A:242 -Pro A:243

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JW6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JW6)

(-) Exons   (0, 0)

(no "Exon" information available for 3JW6)

(-) 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:191
 aligned with PYHD_NPVAC | P04871 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:235
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
           PYHD_NPVAC    11 GRTYVYDNKYYKNLGAVIKNAKRKKHFAEHEIEEATLDPLDNYLVAEDPFLGPGKNQKLTLFKEIRNVKPDTMKLVVGWKGKEFYRETWTRFMEDSFPIVNDQEVMDVFLVVNMRPTRPNRCYKFLAQHALRCDPDYVPHDVIRIVEPSWVGSNNEYRISLAKKGGGCPIMNLHSEYTNSFEQFIDRVIWENFYKPIVYIGTDSAEEEEILLEVSLVFKVKEFAPDAPLFTGPAY 245
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Polyhedrin-3jw6A01                     A:11-244                                                                                                                                                                                           - Pfam domains
         Sec.struct. author ..eeee..eeeehhhhhh--------------------hhhhh...........eeeeeeeeeeeeee...eeee....hhhhhhhhhhhhhhhhhh....eeeeeeeeeeeeeee........eeeeee.-----.....eee....ee.....eeeee..---------------..hhhhhhhh.----....eeeeee.....eeeeeeeeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jw6 A  11 GRTYVYDNKYYKNLDAVI--------------------PLDNYLVAEDPFLGPGKNQKLTLFKEIRNVKPDTmKLVVGWKGKEFYRETWTRFmEDSFPIVNDQEVmDVFLVVNmRPTRPNRCYKFLAQHAL-----YVPHDVIRIVEPSWVGSNNEYRISLA---------------TNSFEQFIDRV----FYKPIVYIGTDSAEEEEILLEVSLVFKVKEFAPDAPLFTGPAY 245
                                    20       | -         -        50        60        70        80  |     90       100  |    110     | 120   |   130       140|     |150       160       170 |       -       190       | -  |    210       220       230       240     
                                            28                   49                                83-MSE             103-MSE      116-MSE 124-MSE          141   147                      172             188       198  203
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  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 3JW6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JW6)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Polyhedrin] (4)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (PYHD_NPVAC | P04871)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0039679    viral occlusion body    A crystalline protein matrix surrounding the nucleocapsids of some insect viruses after their release in the environment. Produced in the host cell, the occlusion body protects the infectious virion after death of the host.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PYHD_NPVAC | P04871: 2wux 2wuy

(-) Related Entries Specified in the PDB File

3jvb POLYHEDRIN PROTEIN OF WISEANA SPP. NUCLEOPOLYHEDROSIS VIRUS