2G33 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Title :   HUMAN HEPATITIS B VIRUS T=4 CAPSID, STRAIN ADYW

Authors :   C. R. Bourne, A. Zlotnick

Date :   17 Feb 06 (Deposition) - 14 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.96

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (60x)

Keywords :   Virus, Capsid, Hepadnavirus, Four-Helix Bundle, Icosahedral (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. R. Bourne, M. G. Finn, A. Zlotnick
Global Structural Changes In Hepatitis B Virus Capsids Induced By The Assembly Effector Hap1.
J. Virol. V. 80 11055 2006
PubMed-ID: 16943288 | Reference-DOI: 10.1128/JVI.00933-06
(for further references see the PDB file header)

Molecule 1 - CORE ANTIGEN
	Chains	:	C, D, B, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11B
	Expression System Strain	:	BL21 DE3 GOLD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ASSEMBLY DOMAIN RESIDUES 1 TO 149
	Gene	:	C
	Mutation	:	YES
	Organism Scientific	:	HEPATITIS B VIRUS SUBTYPE ADYW
	Organism Taxid	:	10419
	Strain	:	ADYW

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (60x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2G33)

(no "Site" information available for 2G33)

(no "SS Bond" information available for 2G33)

(no "Cis Peptide Bond" information available for 2G33)

(no "SAP(SNP)/Variant" information available for 2G33)

(no "PROSITE Motif" information available for 2G33)

(no "Exon" information available for 2G33)

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:148
 aligned with CAPSD_HBVD1 | P03147 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
          CAPSD_HBVD1     1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLPETTV 148
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhh........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g33 A   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLPETTV 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with CAPSD_HBVD1 | P03147 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
          CAPSD_HBVD1     1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLPETT 147
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh....hhhhh......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g33 B   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLPETT 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:147
 aligned with CAPSD_HBVD1 | P03147 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
          CAPSD_HBVD1     1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLPETT 147
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhh........hhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g33 C   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLPETT 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:146
 aligned with CAPSD_HBVD1 | P03147 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
          CAPSD_HBVD1     1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLPET 146
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh...............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhh............hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g33 D   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTLPET 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

(no "SCOP Domain" information available for 2G33)

(no "CATH Domain" information available for 2G33)

(no "Pfam Domain" information available for 2G33)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CAPSD_HBVD1 | P03147)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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.
cellular component
	GO:0039619	T=4 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=4 symmetry. The T=4 capsid is composed of 12 pentameric and 30 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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2g33)

Biological Unit
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	2g33
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	CAPSD_HBVD1 \| P03147
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	CAPSD_HBVD1 \| P03147	:	2g34 2qij 3kxs 4bmg 4g93 5d7y 5e0i 5gmz 5wtw

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