3FBM - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   D431N MUTANT VP2 PROTEIN OF INFECTIOUS BURSAL DISEASE VIRUS; DERIVED T=1 PARTICLES

Authors :   N. Irigoyen, D. Garriga, A. Navarro, N. Verdaguer, J. F. Rodriguez, J. R

Date :   19 Nov 08 (Deposition) - 13 Jan 09 (Release) - 30 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Capsid Protein, Autoproteolytic Activity, Capsid Maturation, Virus Assembly, Ibdv, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Irigoyen, D. Garriga, A. Navarro, N. Verdaguer, J. F. Rodriguez, J. R. Caston
Autoproteolytic Activity Derived From The Infectious Bursal Disease Virus Capsid Protein
J. Biol. Chem. V. 284 8064 2009
PubMed-ID: 19144647 | Reference-DOI: 10.1074/JBC.M808942200

Molecule 1 - POLYPROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Plasmid	:	PESC-URA
	Expression System Strain	:	YPH499
	Expression System Taxid	:	4932
	Expression System Vector Type	:	PLASMID
	Gene	:	CAPSID PROTEIN VP2
	Mutation	:	YES
	Organism Common	:	IBDV
	Organism Scientific	:	AVIAN INFECTIOUS BURSAL DISEASE VIRUS
	Organism Taxid	:	10995
	Strain	:	SOROA
	Synonym	:	VP2 CAPSID PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

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

Biological Unit 1 (0, 0)

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

(no "Site" information available for 3FBM)

(no "SS Bond" information available for 3FBM)

(no "Cis Peptide Bond" information available for 3FBM)

Asymmetric Unit (10, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_POLS_IBDV_001 *	Y	80	L	POLS_IBDV	---	---	A	Y	80	L
02	UniProt	VAR_POLS_IBDV_002 *	H	253	Q	POLS_IBDV	---	---	A	H	253	Q
03	UniProt	VAR_POLS_IBDV_003 *	L	263	F	POLS_IBDV	---	---	A	L	263	F
04	UniProt	VAR_POLS_IBDV_004 *	A	270	T	POLS_IBDV	---	---	A	T	270	T
05	UniProt	VAR_POLS_IBDV_005 *	N	279	D	POLS_IBDV	---	---	A	N	279	D
06	UniProt	VAR_POLS_IBDV_006 *	T	284	A	POLS_IBDV	---	---	A	T	284	A
07	UniProt	VAR_POLS_IBDV_007 *	L	290	M	POLS_IBDV	---	---	A	M	290	M
08	UniProt	VAR_POLS_IBDV_008 *	I	312	V	POLS_IBDV	---	---	A	I	312	V
09	UniProt	VAR_POLS_IBDV_009 *	R	330	S	POLS_IBDV	---	---	A	R	330	S
10	UniProt	VAR_POLS_IBDV_010 *	G	409	A	POLS_IBDV	---	---	A	G	409	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (10, 600)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_POLS_IBDV_001 *	Y	80	L	POLS_IBDV	---	---	A	Y	80	L
02	UniProt	VAR_POLS_IBDV_002 *	H	253	Q	POLS_IBDV	---	---	A	H	253	Q
03	UniProt	VAR_POLS_IBDV_003 *	L	263	F	POLS_IBDV	---	---	A	L	263	F
04	UniProt	VAR_POLS_IBDV_004 *	A	270	T	POLS_IBDV	---	---	A	T	270	T
05	UniProt	VAR_POLS_IBDV_005 *	N	279	D	POLS_IBDV	---	---	A	N	279	D
06	UniProt	VAR_POLS_IBDV_006 *	T	284	A	POLS_IBDV	---	---	A	T	284	A
07	UniProt	VAR_POLS_IBDV_007 *	L	290	M	POLS_IBDV	---	---	A	M	290	M
08	UniProt	VAR_POLS_IBDV_008 *	I	312	V	POLS_IBDV	---	---	A	I	312	V
09	UniProt	VAR_POLS_IBDV_009 *	R	330	S	POLS_IBDV	---	---	A	R	330	S
10	UniProt	VAR_POLS_IBDV_010 *	G	409	A	POLS_IBDV	---	---	A	G	409	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

(no "Exon" information available for 3FBM)

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:428
 aligned with POLS_IBDV | P61825 from UniProtKB/Swiss-Prot  Length:1012

    Alignment length:433
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437   
            POLS_IBDV     8 TQQIVPFIRSLLMPTTGPASIPDDTLEKHTLRSETSTYNLTVGDTGSGLIVFFPGFPGSIVGAHYTLQSNGNYKFDQMLLTAQNLPASYNYCRLVSRSLTVRSSTLPGGVYALNGTINAVTFQGSLSELTDVSYNGLMSATANINDKIGNVLVGEGVTVLSLPTSYDLGYVRLGDPIPAIGLDPKMVATCDSSDRPRVYTITAADDYQFSSQYQPGGVTITLFSANIDAITSLSVGGELVFQTSVHGLVLGATIYLIGFDGTAVITRAVAANNGLTTGTDNLLPFNLVIPTNEITQPITSIKLEIVTSKSGGQAGDQMSWSARGSLAVTIHGGNYPGALRPVTLVAYERVATGSVVTVAGVSNFELIPNPELAKNLVTEYGRFDPGAMNYTKLILSERDRLGIKTVWPTREYTDFREYFMEVADLNSPLKIAG 440
               SCOP domains d3fbma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh............eeeeeeeeeeee......eeeee.......eeeeeeee.....eeeeeeee...hhhh.eeeeeeeeeeeeeeeee..-----...eeeeeee..hhhhh......hhhhh..hhh.eeeeee....eeee..........ee..ee............ee......eeeeeeeeeeeeeee......eeeeeeeeeeee...eeeeeeeeeee....eeeeeeeeeee....eeeeeeeeeeee......eeeeeeeeehhhhh...eeeeeeeeeeee........eeeeeeeeeeeee...........eeeeeee......eeeeeeeeeeeeee..hhhhh..........hhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q---------F------T--------D----A-----M---------------------V-----------------S------------------------------------------------------------------------------A------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fbm A   8 TQQIVPFIRSLLMPTTGPASIPDDTLEKHTLRSETSTYNLTVGDTGSGLIVFFPGFPGSIVGAHYTLQGNGNYKFDQMLLTAQNLPASYNYCRLVSRSLTVRSSTLP-----LNGTINAVTFQGSLSELTDVSYNGLMSATANINDKIGNVLVGEGVTVLSLPTSYDLGYVRLGDPIPAIGLDPKMVATCDSSDRPRVYTITAADDYQFSSQYQPGGVTITLFSANIDAITSLSVGGELVFRTSVHGLVLGATIYLIGFDGTTVITRAVAANNGLTTGTDNLMPFNLVIPTNEITQPITSIKLEIVTSKSGGQAGDQMSWSARGSLAVTIHGGNYPGALRPVTLVAYERVATGSVVTVAGVSNFELIPNPELAKNLVTEYGRFDPGAMNYTKLILSERDRLGIKTVWPTREYTDFREYFMEVANLNSPLKIAG 440
                                    17        27        37        47        57        67        77        87        97       107      |  -  |    127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437   
                                                                                                                                    114   120

Chain A from PDB  Type:PROTEIN  Length:428
 aligned with POLS_IBDVB | Q9WI42 from UniProtKB/Swiss-Prot  Length:1012

    Alignment length:433
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437   
           POLS_IBDVB     8 TQQIVPFIRSLLMPTTGPASIPDDTLEKHTLRSETSTYNLTVGDTGSGLIVFFPGFPGSIVGAHYTLQGNGNYKFDQMLLTAQNLPASYNYCRLVSRSLTVRSSTLPGGVYALNGTINAVTFQGSLSELTDVSYNGLMSATANINDKIGNVLVGEGVTVLSLPTSYDLGYVRLGDPIPAIGLDPKMVATCDSSDRPRVYTITAADDYQFSSQYQPGGVTITLFSANIDAITSLSVGGELVFRTSVHGLVLGATIYLIGFDGTTVITRAVAANNGLTTGTDNLMPFNLVIPTNEITQPITSIKLEIVTSKSGGQAGDQMSWSARGSLAVTIHGGNYPGALRPVTLVAYERVATGSVVTVAGVSNFELIPNPELAKNLVTEYGRFDPGAMNYTKLILSERDRLGIKTVWPTREYTDFREYFMEVADLNSPLKIAG 440
               SCOP domains d3fbma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh............eeeeeeeeeeee......eeeee.......eeeeeeee.....eeeeeeee...hhhh.eeeeeeeeeeeeeeeee..-----...eeeeeee..hhhhh......hhhhh..hhh.eeeeee....eeee..........ee..ee............ee......eeeeeeeeeeeeeee......eeeeeeeeeeee...eeeeeeeeeee....eeeeeeeeeee....eeeeeeeeeeee......eeeeeeeeehhhhh...eeeeeeeeeeee........eeeeeeeeeeeee...........eeeeeee......eeeeeeeeeeeeee..hhhhh..........hhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q---------F------T--------D----A-----M---------------------V-----------------S------------------------------------------------------------------------------A------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fbm A   8 TQQIVPFIRSLLMPTTGPASIPDDTLEKHTLRSETSTYNLTVGDTGSGLIVFFPGFPGSIVGAHYTLQGNGNYKFDQMLLTAQNLPASYNYCRLVSRSLTVRSSTLP-----LNGTINAVTFQGSLSELTDVSYNGLMSATANINDKIGNVLVGEGVTVLSLPTSYDLGYVRLGDPIPAIGLDPKMVATCDSSDRPRVYTITAADDYQFSSQYQPGGVTITLFSANIDAITSLSVGGELVFRTSVHGLVLGATIYLIGFDGTTVITRAVAANNGLTTGTDNLMPFNLVIPTNEITQPITSIKLEIVTSKSGGQAGDQMSWSARGSLAVTIHGGNYPGALRPVTLVAYERVATGSVVTVAGVSNFELIPNPELAKNLVTEYGRFDPGAMNYTKLILSERDRLGIKTVWPTREYTDFREYFMEVANLNSPLKIAG 440
                                    17        27        37        47        57        67        77        87        97       107      |  -  |    127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437   
                                                                                                                                    114   120

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: Positive stranded ssRNA viruses (163)

Family: Birnaviridae-like VP (6)

Protein domain: automated matches (3)

Avian infectious bursal disease virus [TaxId: 10995] (1)

d3fbma_

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

(no "Pfam Domain" information available for 3FBM)

Asymmetric Unit(hide GO term definitions)

Chain A (POLS_IBDVB | Q9WI42)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0039621	T=13 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=13 symmetry. The T=13 capsid is composed of 12 pentameric and 120 hexameric capsomeres.
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	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.

Chain A (POLS_IBDV | P61825)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0039621	T=13 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=13 symmetry. The T=13 capsid is composed of 12 pentameric and 120 hexameric capsomeres.
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	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
(no "Cis Peptide Bonds" information available for 3fbm)

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	3fbm
		Family and Domain Information	:	ProDom \| SYSTERS
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	POLS_IBDV \| P61825
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	POLS_IBDVB \| Q9WI42
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	POLS_IBDV \| P61825
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UniProtKB/Swiss-Prot
	POLS_IBDV \| P61825	:	2gsy 2imu

2gsy	INFECTIOUS BURSAL DISEASE VIRUS DERIVED T=1 PARTICLES, NATIVE VP2 PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (10, 10)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

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Gene Ontology (10, 20)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File