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Title :   CRYSTAL STRUCTURE OF HBV CAPSID MUTANT DIMER (OXY FORM), STRAIN ADYW

Authors :   C. Packianathan, S. P. Katen, A. Zlotnick

Date :   03 Dec 09 (Deposition) - 02 Feb 10 (Release) - 02 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: E,F  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Core Protein, Capsid, Hepadnavirus, Four Helix Bundle, Icosahedral, Dimer, Capsid Protein, Dna-Binding, Host Cytoplasm, Host-Virus Interaction, Phosphoprotein, Rna- Binding, Virion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Packianathan, S. P. Katen, C. E. Dann, A. Zlotnick
Conformational Changes In The Hepatitis B Virus Core Protein Are Consistent With A Role For Allostery In Virus Assembly
J. Virol. V. 84 1607 2010
PubMed-ID: 19939922 | Reference-DOI: 10.1128/JVI.02033-09
(for further references see the PDB file header)

Molecule 1 - CAPSID PROTEIN
	Chains	:	F, E, C, D, A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11C
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ASSEMBLY DOMAIN RESIDUES 1 TO 149
	Gene	:	C
	Mutation	:	YES
	Organism Common	:	HBV-D
	Organism Scientific	:	HEPATITIS B VIRUS SUBTYPE ADYW
	Organism Taxid	:	10419
	Strain	:	ADYW
	Synonym	:	CORE PROTEIN, CORE ANTIGEN, HBCAG, P21.5

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:					E	F
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3KXS)

(no "Site" information available for 3KXS)

Asymmetric Unit

No.	Residues
1	A:61	-	B:61
2	C:61	-	D:61
3	E:61	-	F:61

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

(no "SAP(SNP)/Variant" information available for 3KXS)

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

(no "Exon" information available for 3KXS)

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:140
 aligned with CAPSD_HBVD1 | P03147 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
          CAPSD_HBVD1     1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPIL 140
               SCOP domains d3kxsa_ A: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxs A   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPIL 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with CAPSD_HBVD1 | P03147 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  
          CAPSD_HBVD1     1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILST 142
               SCOP domains d3kxsb_ B: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhh........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxs B   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILST 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:142
 aligned with CAPSD_HBVD1 | P03147 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  
          CAPSD_HBVD1     1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILST 142
               SCOP domains d3kxsc_ C: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxs C   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILST 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:141
 aligned with CAPSD_HBVD1 | P03147 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
          CAPSD_HBVD1     1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILS 141
               SCOP domains d3kxsd_ D: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxs D   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILS 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain E from PDB  Type:PROTEIN  Length:143
 aligned with CAPSD_HBVD1 | P03147 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   
          CAPSD_HBVD1     1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTL 143
               SCOP domains d3kxse_ E: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxs E   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTL 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain F from PDB  Type:PROTEIN  Length:142
 aligned with CAPSD_HBVD1 | P03147 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  
          CAPSD_HBVD1     1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILST 142
               SCOP domains d3kxsf_ F: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Hepatitis_core-3kxsF01 F:2-142                                                                                                                Pfam domains (1)
           Pfam domains (2) -Hepatitis_core-3kxsF02 F:2-142                                                                                                                Pfam domains (2)
           Pfam domains (3) -Hepatitis_core-3kxsF03 F:2-142                                                                                                                Pfam domains (3)
           Pfam domains (4) -Hepatitis_core-3kxsF04 F:2-142                                                                                                                Pfam domains (4)
           Pfam domains (5) -Hepatitis_core-3kxsF05 F:2-142                                                                                                                Pfam domains (5)
           Pfam domains (6) -Hepatitis_core-3kxsF06 F:2-142                                                                                                                Pfam domains (6)
         Sec.struct. author .....hhhhh.hhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kxs F   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILST 142
                                    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)
		→ 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 alpha proteins (14657)

Fold: Hepatitis B viral capsid (hbcag) (3)

Superfamily: Hepatitis B viral capsid (hbcag) (3)

Family: Hepatitis B viral capsid (hbcag) (3)

Protein domain: automated matches (2)

Hepatitis b virus [TaxId: 10419] (1)

1a	d3kxsa_	A:
1b	d3kxsb_	B:
1c	d3kxsc_	C:
1d	d3kxsd_	D:
1e	d3kxse_	E:
1f	d3kxsf_	F:

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (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.

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(no "Cis Peptide Bonds" information available for 3kxs)

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

2g33	T=4 CAPSID OF 120 ASSEMBLY DOMAIN DIMERS
2g34	T=4 CAPSID OF 120 ASSEMBLY DOMAIN DIMERS COMPLEXED WITH THE ASSEMBLY EFFECTOR HAP1

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (3, 3)

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