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(-) Description

Title :  STRUCTURAL DETERMINANTS OF TISSUE TROPISM AND IN VIVO PATHOGENICITY FOR THE PARVOVIRUS MINUTE VIRUS OF MICE
 
Authors :  M. Kontou, L. Govindasamy, H. J. Nam, N. Bryant, A. L. Llamas-Saiz, C. Foces-Foces, E. Hernando, M. P. Rubio, R. Mckenna, J. M. Almendral, M. Agbandje-Mckenna
Date :  03 Mar 05  (Deposition) - 06 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Immunosuppressive Strain, Mvmi, Minute Virus Of Mice, Icosahedral Virus, Virus/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kontou, L. Govindasamy, H. J. Nam, N. Bryant, A. L. Llamas-Saiz, C. Foces-Foces, E. Hernando, M. P. Rubio, R. Mckenna, J. M. Almendral, M. Agbandje-Mckenna
Structural Determinants Of Tissue Tropism And In Vivo Pathogenicity For The Parvovirus Minute Virus Of Mice.
J. Virol. V. 79 10931 2005
PubMed-ID: 16103145  |  Reference-DOI: 10.1128/JVI.79.17.10931-10943.2005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAT PROTEIN VP2
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Strain: IMMUNOSUPPRESSIVE STRAIN
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Organism Scientific: MURINE MINUTE VIRUS (STRAIN MVMI)
    Organism Taxid: 10795
    Strain: MVMI
 
Molecule 2 - 5'-D(*AP*TP*CP*CP*TP*CP*TP*AP*TP*CP*AP*C)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2D5M1Ligand/Ion2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 60)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2D5M60Ligand/Ion2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC B:6 , DC B:8 , DT B:9 , DT B:11BINDING SITE FOR RESIDUE CA B 201
2AC2SOFTWAREDT B:4 , DC B:5 , DT B:11BINDING SITE FOR RESIDUE CA B 202
3AC3SOFTWAREDA B:10 , DC B:12 , DA B:13 , DC B:14BINDING SITE FOR RESIDUE D5M B 231

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z1C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z1C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z1C)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z1C)

(-) 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:549
 aligned with CAPSD_MUMIM | P07302 from UniProtKB/Swiss-Prot  Length:729

    Alignment length:549
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720         
          CAPSD_MUMIM   181 GVGVSTGSYDNQTHYRFLGDGWVEITALATRLVHLNMPKSENYCRIRVHNTTDTSVKGNMAKDDAHEQIWTPWSLVDANAWGVWLQPSDWQYICNTMSQLNLVSLDQEIFNVVLKTVTEQDSGGQAIKIYNNDLTACMMVAVDSNNILPYTPAANSMETLGFYPWKPTIASPYRYYFCVDRDLSVTYENQEGTIEHNVMGTPKGMNSQFFTIENTQQITLLRTGDEFATGTYYFDTNPVKLTHTWQTNRQLGQPPLLSTFPEADTDAGTLTAQGSRHGATQMEVNWVSEAIRTRPAQVGFCQPHNDFEASRAGPFAAPKVPADVTQGVDREANGSVRYSYGKQHGENWAAHGPAPERYTWDETNFGSGRDTRDGFIQSAPLVVPPPLNGILTNANPIGTKNDIHFSNVFNSYGPLTAFSHPSPVYPQGQIWDKELDLEHKPRLHITAPFVCKNNAPGQMLVRLGPNLTDQYDPNGATLSRIVTYGTFFWKGKLTMRAKLRANTTWNPVYQVSVEDNGNSYMSVTKWLPTATGNMQSVPLITRPVARNTY 729
               SCOP domains d1z1ca1 A:39-587 Parvovirus (panleukopenia virus) capsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1z1cA00 A:39-587 Empty Capsid Viral Protein 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains Parvo_coat-1z1cA01 A:39-568                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ------------------- Pfam domains
         Sec.struct. author ............eeeee....eeeeeeeeeeeeeee.......ee....hhhhhh............eeeeeeee....hhhhhhhhhhhhhhhhheeeeeeeeeeeeeeeeeeeeee..........eeee.....eeeeee........hhhhhh..........ee.eeeeee..........................hhhhh...hhhhhh..eee....eee...ee.....ee.ee...hhhhh.............................................ee........eeee..eeee.............hhhhh.eee...................eee...............ee............ee............hhhhhh......ee.............ee................ee.......eeeeee....................eeeeeeeeeeeeeeee......................hhhhhh................ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z1c A  39 GVGVSTGSYDNQTHYRFLGDGWVEITALATRLVHLNMPKSENYCRIRVHNTTDTSVKGNMAKDDAHEQIWTPWSLVDANAWGVWLQPSDWQYICNTMSQLNLVSLDQEIFNVVLKTVTEQDSGGQAIKIYNNDLTACMMVAVDSNNILPYTPAANSMETLGFYPWKPTIASPYRYYFCVDRDLSVTYENQEGTIEHNVMGTPKGMNSQFFTIENTQQITLLRTGDEFATGTYYFDTNPVKLTHTWQTNRQLGQPPLLSTFPEADTDAGTLTAQGSRHGATQMEVNWVSEAIRTRPAQVGFCQPHNDFEASRAGPFAAPKVPADVTQGMDREANGSVRYSYGKQHGENWAAHGPAPERYTWDETNFGSGRDTRDGFIQSAPLVVPPPLNGILTNANPIGTKNDIHFSNVFNSYGPLTTFSHPSPVYPQGQIWDKELDLEHKPRLHITAPFVCKNNAPGQMLVRLGPNLTDQYDPNGATLSRIVTYGTFFWKGKLTMRAKLRANTTWNPVYQVSVEDNGNSYMSVTKWLPTATGNMQSVPLITRPVARNTY 587
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578         


Chain B from PDB  Type:DNA  Length:12
                                            
                 1z1c B   3 ATCCTCTATCAC  14
                                    12  


Chain C from PDB  Type:DNA  Length:9
                                         
                 1z1c C  15 ACACCAAAA  23
   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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Parvo_coat] (8)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (CAPSD_MUMIM | P07302)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0075521    microtubule-dependent intracellular transport of viral material towards nucleus    The directed movement of a virus, or part of a virus, towards the host cell nucleus using host microtubules.
    GO:0039665    permeabilization of host organelle membrane involved in viral entry into host cell    Induction of organellar membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with a viral capsid. Results in release of the virus contents from an organelle into the host cell cytoplasm.
    GO:0075606    transport of viral material towards nucleus    The directed movement of a virus, or part of a virus, towards the host cell nucleus. The process begins after viral entry, and ends when the viral material is at the nuclear membrane.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0039615    T=1 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=1 symmetry. The T=1 capsid is composed of 12 pentameric capsomeres.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_MUMIM | P07302: 1mvm 2xgk

(-) Related Entries Specified in the PDB File

1mvm REFINED COORDINATES
1z14