1C8G - JenaLib

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Title :   FELINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE

Authors :   M. G. Rossmann, A. A. Simpson

Date :   05 May 00 (Deposition) - 09 Aug 00 (Release) - 30 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (60x)

Keywords :   Beta Barrel, Protein-Dna Complex, Double Complex, Icosahedral Virus, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Simpson, V. Chandrasekar, B. Hebert, G. M. Sullivan, M. G. Rossmann, C. R. Parrish
Host Range And Variability Of Calcium Binding By Surface Loops In The Capsids Of Canine And Feline Parvoviruses.
J. Mol. Biol. V. 300 597 2000
PubMed-ID: 10884355 | Reference-DOI: 10.1006/JMBI.2000.3868
(for further references see the PDB file header)

Molecule 1 - FELINE PANLEUKOPENIA VIRUS CAPSID
	Chains	:	A
	Organism Scientific	:	FELINE PANLEUKOPENIA VIRUS
	Organism Taxid	:	10786

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:405	BINDING SITE FOR RESIDUE CA A 586

Asymmetric Unit

No.	Residues
1	A:490	-	A:494

Asymmetric Unit

No.	Residues
1	Pro A:160	-	Pro A:161
2	Leu A:422	-	Pro A:423
3	Tyr A:464	-	Pro A:465

(no "SAP(SNP)/Variant" information available for 1C8G)

(no "PROSITE Motif" information available for 1C8G)

(no "Exon" information available for 1C8G)

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
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Chain A from PDB  Type:PROTEIN  Length:548
 aligned with CAPSD_FPV19 | P24840 from UniProtKB/Swiss-Prot  Length:727

    Alignment length:548
                                   189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719        
          CAPSD_FPV19   180 GVGISTGTFNNQTEFKFLENGWVEITANSSRLVHLNMPESENYKRVVVNNMDKTAVKGNMALDDIHVQIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSFEQEIFNVVLKTVSESATQPPTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWKPTIPTPWRYYFQWDRTLIPSHTGTSGTPTNVYHGTDPDDVQFYTIENSVPVHLLRTGDEFATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGNTDYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGDPRYAFGRQHGQKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTGINYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQLFVKVAPNLTNEYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNYVPNNIGAMKIVYEKSQLAPRKLY 727
               SCOP domains d1c8ga_ A: Parvovirus (panleukopenia virus) capsid protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1c8gA00 A:37-584 Empty Capsid Viral Protein 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee....eeeeeeeeeeeeeee.......eeeee.hhhhhh...hhhhh..eeeeeeeeee....hhhhh.hhhhhhhhhhheeeeeeeeeeeeeeeeeeeeee..................eeeeee........hhhhhh.............eeeeee...eeee............eeeee.hhhhh...hhhhhh.eeee.....ee...ee.....ee..ee..hhhhh.......................hhhhh.....................ee........eeee..eeee......................eeee...............eeee.........hhhhh.ee........hhh.ee........................ee......ee.....eee...............eee......eeeeee....................eeeeeeeeeeeeeeeee.................hhhhh............ee....ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c8g A  37 GVGISTGTFNNQTEFKFLENGWVEITANSSRLVHLNMPESENYKRVVVNNMDKTAVKGNMALDDIHVEIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSFEQEIFNVVLKTVSESATQPPTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWKPTIPTPWRYYFQWDRTLIPSHTGTSGTPTNVYHGTDPDDVQFYTIENSVPVHLLRTGDEFATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGNTDYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGDPRYAFGRQHGQKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTGINYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHINAPFVCQNNCPGQLFVKVAPNLTNQYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNYVPNNIGAMKIVYEKSQLAPRKLY 584
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) (278)

Superfamily: ssDNA viruses (39)

Family: Parvoviridae-like VP (31)

Protein domain: Parvovirus (panleukopenia virus) capsid protein (15)

Feline parvovirus [TaxId: 10785] (3)

d1c8ga_

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Complex (381)

Topology: Empty Capsid Viral Protein 2 (22)

Homologous Superfamily: Empty Capsid Viral Protein 2 (22)

Feline panleukopenia virus. Organism_taxid: 10786 (2)

1c8gA00

A:37-584

(no "Pfam Domain" information available for 1C8G)

Asymmetric Unit(hide GO term definitions)

Chain A (CAPSD_FPV19 | P24840)

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.

Asymmetric Unit
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	Sites
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	Cis Peptide Bonds
		Leu A:422 - Pro A:423	[ RasMol ]
		Pro A:160 - Pro A:161	[ RasMol ]
		Tyr A:464 - Pro A:465	[ RasMol ]

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	1c8g
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	CAPSD_FPV19 \| P24840
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UniProtKB/Swiss-Prot
	CAPSD_FPV19 \| P24840	:	1c8e 1c8f 1fpv

1c8d	CONTAINS THE REFINED STRUCTURE OF THE A300D MUTANT OF CANINE PARVOVIRUS
1c8e	CONTAINS THE CLOSELY RELATED FELINE PANLEUKOPENIA VIRUS, IN THE PRESENCE OF EDTA
1c8f	CONTAINS THE REFINED STRUCTURE OF FELINE PANLEUKOPENIA VIRUS AT PH 7.5
1c8h	CONTAINS THE REFINED STRUCTURE OF CANINE PARVOVIRUS AT PH 5.5
1fpv	CONTAINS THE CLOSELY RELATED FELINE PANLEUKOPENIA VIRUS
1ijs	CONTAINS AN UNREFINED VERSION OF THIS STRUCTURE
1mvm	CONTAINS THE RELATED MINUTE VIRUS OF MOUSE
2cas	CONTAINS THE WILD TYPE FORM OF THIS VIRUS
4dpv	CONTAINS THE WILD TYPE FORM OF THIS VIRUS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (1, 1)

SS Bonds (1, 1)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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