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(-) Description

Title :  STRUCTURAL CHARACTERIZATION OF H-1 PARVOVIRUS: COMPARISON OF INFECTIOUS VIRIONS TO REPLICATION DEFECTIVE PARTICLES
 
Authors :  S. Halder, H-J. Nam, L. Govindasamy, M. Vogel, C. Dinsart, N. Salome, R. M. Agbandje-Mckenna
Date :  27 Jul 12  (Deposition) - 27 Feb 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (60x)
Keywords :  Beta-Barrel, Icosahedral Virus, Virus, Capsid, Capsid Proteins, Parvovirus, Beta-Barrel, Capsid Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Halder, H. J. Nam, L. Govindasamy, M. Vogel, C. Dinsart, N. Salome, R. Mckenna, M. Agbandje-Mckenna
Structural Characterization Of H-1 Parvovirus: Comparison O Infectious Virions To Empty Capsids.
J. Virol. V. 87 5128 2013
PubMed-ID: 23449783  |  Reference-DOI: 10.1128/JVI.03416-12

(-) Compounds

Molecule 1 - CAPSID PROTEIN VP1
    Chains: A
    Organism Scientific: H-1 PARVOVIRUS
    Organism Taxid: 10799
    Other Details: INFECTION IN NB324K CELLS
    Synonym: COAT PROTEIN VP1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:374 , ASP A:375BINDING SITE FOR RESIDUE NA A 601
2AC2SOFTWAREGLN A:148 , THR A:272BINDING SITE FOR RESIDUE CL A 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1His A:348 -Asp A:349
2Ala A:423 -Pro A:424
3Ile A:427 -Pro A:428
4Tyr A:469 -Pro A:470

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GBT)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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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:552
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............................................................hhhhh................hhhhhhhhhhhhhhhhh....................................................hhhhhh......................................................hhhhhh..............................hhhhh....................hhhhh......................................................hhhhh......hhhhh........................hhhh............hhh.......hhhhh...hhhhh.................................................................................................................hhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gbt A  38 GIGVSTGTYDNQTTYKFLGDGWVEITAHASRLLHLGMPPSENYCRVTVHNNQTTGHGTKVKGNMAYDDTHQQIWTPWSLVDANAWGVWFQPSDWQFIQNSMESLNLDSLSQELFNVVVKTVTEQQGAIKVYNNDLTACMMVALDSNNILPYTPAAQTSETLGFYPWKPTAPAPYRYYFFMPRQLSVTSSNSAEGTQITDTIGEPQALNSQFFTIENTLPITLLRTGDEFTTGTYIFNTDPLKLTHTWQTNRHLGMPPRITDLPTSDTATASLTANGDRFGSTQTQNVNYVTEALRTRPAQIGFMQPHDNFEANRGGPFKVPVVPLDITAGEDHDANGAIRFNYGKQHGEDWAKQGAAPERYTWDAIDSAAGRDTARCFVQSAPISIPPNQNQILQREDAIAGRTNMHYTNVFNSYGPLSAFPHPDPIYPNGQIWDKELDLEHKPRLHVTAPFVCKNNPPGQLFVRLGPNLTDQFDPNSTTVSRIVTYSTFYWKGILKFKAKLRPNLTWNPVYQATTDSVANSYMNVKKWLPSATGNMHSDPLICRPVPHMTY 593
                                    47        57        67        77        87        97       107       117       127       137       147       157     ||171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591  
                                                                                                                                                       163|                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                        168
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4GBT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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  4gbt
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  CAPSD_PAVHH | P03136
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_PAVHH | P03136: 4g0r

(-) Related Entries Specified in the PDB File

4g0r