PDB-6ecs: Crystal structure of WHV core protein mutant Y132A dimer

ID or keywords:

Entry

Database: PDB / ID: 6ecs

Title

Crystal structure of WHV core protein mutant Y132A dimer

Components

External core antigen

Keywords

VIRAL PROTEIN / WHV / Core protein dimer

Function / homology

Function and homology information

microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / virus-mediated perturbation of host defense response / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / structural molecule activity /

DNA binding /

RNA binding / extracellular region
Similarity search - Function

Biological species

Woodchuck hepatitis B virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Zhao, Z. / Gonzalez-Gutierrez, G. / Zlotnick, A.

Funding support

United States, 1items

Citation

Journal: J Virol / Year: 2019
Title: Structural Differences between the Woodchuck Hepatitis Virus Core Protein in the Dimer and Capsid States Are Consistent with Entropic and Conformational Regulation of Assembly.
Authors: Zhongchao Zhao / Joseph Che-Yen Wang / Giovanni Gonzalez-Gutierrez / Balasubramanian Venkatakrishnan / Roi Asor / Daniel Khaykelson / Uri Raviv / Adam Zlotnick /

Abstract: Hepadnaviruses are hepatotropic enveloped DNA viruses with an icosahedral capsid. Hepatitis B virus (HBV) causes chronic infection in an estimated 240 million people; woodchuck hepatitis virus (WHV), ...Hepadnaviruses are hepatotropic enveloped DNA viruses with an icosahedral capsid. Hepatitis B virus (HBV) causes chronic infection in an estimated 240 million people; woodchuck hepatitis virus (WHV), an HBV homologue, has been an important model system for drug development. The dimeric capsid protein (Cp) has multiple functions during the viral life cycle and thus has become an important target for a new generation of antivirals. Purified HBV and WHV Cp spontaneously assemble into 120-dimer capsids. Though they have 65% identity, WHV Cp has error-prone assembly with stronger protein-protein association. We have taken advantage of the differences in assemblies to investigate the basis of assembly regulation. We determined the structures of the WHV capsid to 4.5-Å resolution by cryo-electron microscopy (cryo-EM) and of the WHV Cp dimer to 2.9-Å resolution by crystallography and examined the biophysical properties of the dimer. We found, in dimer, that the subdomain that makes protein-protein interactions is partially disordered and rotated 21° from its position in capsid. This subdomain is susceptible to proteolysis, consistent with local disorder. WHV assembly shows similar susceptibility to HBV antiviral molecules, suggesting that HBV assembly follows similar transitions. These data show that there is an entropic cost for assembly that is compensated for by the energetic gain of burying hydrophobic interprotein contacts. We propose a series of stages in assembly that incorporate a disorder-to-order transition and structural shifts. We suggest that a cascade of structural changes may be a common mechanism for regulating high-fidelity capsid assembly in HBV and other viruses. Virus capsids assemble spontaneously with surprisingly high fidelity. This requires strict geometry and a narrow range of association energies for these protein-protein interactions. It was hypothesized that requiring subunits to undergo a conformational change to become assembly active could regulate assembly by creating an energetic barrier and attenuating association. We found that woodchuck hepatitis virus capsid protein undergoes structural transitions between its dimeric and its 120-dimer capsid states. It is likely that the closely related hepatitis B virus capsid protein undergoes similar structural changes, which has implications for drug design. Regulation of assembly by structural transition may be a common mechanism for many viruses.

History

Deposition	Aug 8, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 1, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2019	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ecs.cif.gz	234.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6ecs.ent.gz	191.8 KB	Display	PDB format
PDBx/mmJSON format	6ecs.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ec/6ecs ftp://data.pdbj.org/pub/pdb/validation_reports/ec/6ecs	HTTPS FTP

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Related structure data

Related structure data	9031C 6edjC 3kxsS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3kxs-3 3kxs-2 3zxa-d 6pe9-5 4bmg-3 5ypr-d 5cp2-1 3s24-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#62 - Feb 2005 Major Histocompatibility Complex similarity (3) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: External core antigen

B: External core antigen

C: External core antigen

D: External core antigen

68.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: External core antigen

B: External core antigen

defined by author&software
Evidence: gel filtration, native gel electrophoresis
34.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: External core antigen

D: External core antigen

defined by author&software
34.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.410, 116.410, 161.760
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	External core antigen / HBeAg / Precore protein / p25 Mass: 17034.369 Da / Num. of mol.: 4 / Mutation: Y132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Woodchuck hepatitis B virus / Production host: Escherichia coli (E. coli) / References: UniProt: P0C6J2

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.64 Å³/Da / Density % sol: 73.51 %
Crystal grow	Temperature: 296.35 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 13% polyethylene glycol 400, 240 mM KCl and 50 mM MES (pH 5.8)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 10, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.9→63.09 Å / Num. obs: 28665 / % possible obs: 99.93 % / Redundancy: 10.9 % / B_iso Wilson estimate: 78.95 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.1083 / R_pim(I) all: 0.0342 / R_rim(I) all: 0.1136 / Net I/σ(I): 19.47
Reflection shell	Resolution: 2.9→3.004 Å / Redundancy: 9.9 % / R_merge(I) obs: 1.638 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 2817 / CC_1/2: 0.589 / R_pim(I) all: 0.5449 / R_rim(I) all: 1.728 / % possible all: 99.93

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KXS

3kxs

Resolution: 2.9→63.087 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 24.58

	R_factor	Num. reflection	% reflection
R_free	0.2279	3795	6.99 %
R_work	0.1983	-	-
obs	0.2004	28656	99.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 84.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→63.087 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4393	0	0	0	4393

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4526
X-RAY DIFFRACTION	f_angle_d	0.859	6188
X-RAY DIFFRACTION	f_dihedral_angle_d	7.723	2621
X-RAY DIFFRACTION	f_chiral_restr	0.046	699
X-RAY DIFFRACTION	f_plane_restr	0.005	778

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.9002-2.9369	0.4057	144	0.3789	1887	X-RAY DIFFRACTION	99
2.9369-2.9755	0.3915	131	0.3375	1889	X-RAY DIFFRACTION	100
2.9755-3.0163	0.3543	140	0.3237	1839	X-RAY DIFFRACTION	100
3.0163-3.0594	0.3253	150	0.3104	1883	X-RAY DIFFRACTION	100
3.0594-3.105	0.3282	134	0.3007	1852	X-RAY DIFFRACTION	100
3.105-3.1535	0.3332	136	0.2919	1912	X-RAY DIFFRACTION	100
3.1535-3.2052	0.3132	143	0.2837	1803	X-RAY DIFFRACTION	100
3.2052-3.2605	0.3739	138	0.2751	1897	X-RAY DIFFRACTION	100
3.2605-3.3198	0.2788	140	0.2509	1883	X-RAY DIFFRACTION	100
3.3198-3.3836	0.2855	144	0.2464	1850	X-RAY DIFFRACTION	100
3.3836-3.4527	0.26	142	0.2432	1852	X-RAY DIFFRACTION	100
3.4527-3.5278	0.295	140	0.2189	1895	X-RAY DIFFRACTION	100
3.5278-3.6098	0.2792	135	0.21	1834	X-RAY DIFFRACTION	100
3.6098-3.7001	0.2469	142	0.2039	1913	X-RAY DIFFRACTION	100
3.7001-3.8001	0.2216	132	0.195	1863	X-RAY DIFFRACTION	100
3.8001-3.9119	0.2228	146	0.1984	1900	X-RAY DIFFRACTION	100
3.9119-4.0382	0.2001	136	0.1848	1863	X-RAY DIFFRACTION	100
4.0382-4.1825	0.2428	146	0.17	1851	X-RAY DIFFRACTION	100
4.1825-4.3499	0.2212	142	0.165	1871	X-RAY DIFFRACTION	100
4.3499-4.5478	0.1571	142	0.1484	1858	X-RAY DIFFRACTION	100
4.5478-4.7875	0.1762	128	0.1534	1905	X-RAY DIFFRACTION	100
4.7875-5.0873	0.1748	136	0.1546	1873	X-RAY DIFFRACTION	100
5.0873-5.4799	0.2053	147	0.1715	1887	X-RAY DIFFRACTION	100
5.4799-6.031	0.224	142	0.186	1853	X-RAY DIFFRACTION	100
6.031-6.9028	0.2195	154	0.2121	1865	X-RAY DIFFRACTION	100
6.9028-8.6932	0.1941	146	0.1804	1868	X-RAY DIFFRACTION	100
8.6932-63.1017	0.1833	139	0.1719	1862	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.6244	1.6673	5.7487	0.7498	1.2534	6.3807	-0.5255	-0.5713	0.4366	0.0289	-0.0392	0.2935	-0.2034	-0.2996	0.5551	0.523	-0.0613	0.0962	0.6617	-0.0743	0.5406	-60.4279	17.4668	-3.9034
2	1.8614	-0.9532	-2.2676	2.6709	0.5768	7.2569	0.2389	-0.0395	0.0566	-0.2405	0.2829	-0.6529	-0.4215	1.1129	-0.5322	0.4905	-0.0146	0.0296	0.7188	0.0227	0.6209	-45.6888	16.4491	-14.5985
3	1.9349	0.3823	0.352	4.5383	-0.3546	4.3865	0.0214	-0.0571	0.4061	-0.0788	0.4961	0.5669	-0.7454	0.2848	-0.3471	0.5847	-0.0675	0.0871	0.544	-0.035	0.452	-53.1312	27.039	-19.8843
4	4.5428	1.1977	0.7497	2.2053	-0.195	3.4072	-0.0787	-0.4244	-0.1878	0.6318	-0.1582	-0.702	-0.9776	0.4328	0.3568	1.0264	-0.0313	0.0122	0.6465	-0.0097	1.0471	-50.5679	41.2172	-12.5797
5	2.6654	-0.5509	-0.3454	2.3367	1.4292	4.0063	-0.0191	-0.2097	-0.3471	0.3836	-0.1786	0.0611	0.4393	0.2119	0.2008	0.5619	-0.0987	-0.0106	0.4734	0.0324	0.4269	-50.3862	15.7247	1.3694
6	2.2288	-0.4668	1.3051	2.5666	1.163	2.6664	-1.1957	-0.6908	-0.162	-0.5676	0.4326	-0.2809	-1.3244	2.8759	0.9249	0.7197	-0.0693	-0.0595	1.0668	-0.0511	0.7443	-41.6526	13.3773	-1.0956
7	6.6563	-1.7037	5.7094	3.8996	1.8687	8.6476	0.0005	0.6662	0.1552	-0.7397	-0.2438	-0.2829	-0.0063	0.6052	0.3554	0.6437	0.0641	0.109	0.6405	0.0734	0.5638	-54.5778	15.7329	-27.3665
8	9.6556	-1.8524	3.4874	3.7899	-3.8189	4.1213	0.5502	1.362	0.4607	0.8736	-1.2515	0.0947	-0.3098	2.2139	0.4109	0.8082	-0.0516	0.0173	0.8368	0.1248	0.48	-59.8743	21.148	-35.2075
9	9.0899	4.021	-3.9157	4.7993	-2.9529	2.1669	0.6487	0.2313	0.675	-0.4832	0.0955	0.5575	-0.3064	-1.205	-1.2663	0.7377	0.1488	-0.066	0.5825	0.103	0.6663	-70.6858	25.5756	-32.3396
10	3.1766	1.1701	0.0743	4.2441	-0.7601	4.4034	0.1073	-0.0284	0.2723	0.6061	0.0948	0.5387	-0.4788	-0.3621	-0.1517	0.5861	0.0949	0.0681	0.6153	0.0562	0.461	-66.7891	21.8572	-14.3083
11	4.2772	-0.9529	0.7618	3.3888	-2.414	1.7625	0.1307	-0.127	0.0797	-0.419	-0.521	0.2158	-0.4939	0.012	0.3289	0.8433	-0.0386	0.0296	0.5383	0.0823	0.8686	-63.5329	41.9519	-21.1436
12	1.6766	-0.7248	-1.67	2.1107	-1.6008	4.4708	-0.2245	0.2635	0.1891	-0.7041	0.5795	1.0894	-0.3418	-0.6989	-0.2771	0.6575	0.0212	-0.0786	0.6228	0.1078	0.5333	-67.1365	19.4294	-25.7049
13	7.5608	4.9219	-5.6663	5.4491	-5.5701	5.8605	-0.6021	0.6476	-1.0325	-0.6293	0.4517	-0.5259	1.7557	-0.8656	0.1739	0.9768	0.0183	-0.0512	0.5959	-0.0211	0.6191	-65.5291	13.4589	-38.5441
14	2.2131	-3.2777	-1.1401	5.0604	1.9312	2.8859	0.5386	0.193	0.6688	-1.3523	0.8371	-0.287	0.5266	-1.104	-1.6576	0.7124	-0.1167	-0.1838	0.9324	0.106	0.557	-70.5439	17.7325	-47.3649
15	3.303	0.4955	1.2582	3.7271	-0.8939	3.328	0.4225	-0.2871	0.7169	0.036	0.0252	-0.444	-0.2877	0.4864	-0.3311	0.6271	-0.0743	0.1575	0.6889	-0.2025	0.9237	-51.0367	-8.9445	-7.097
16	4.3932	1.7602	-1.0218	4.3466	-1.2895	1.4296	0.3179	-0.5726	0.7842	0.0227	-0.106	-0.2814	-0.2517	0.3151	-0.2058	0.5099	-0.0406	0.1472	0.5808	-0.1541	0.5988	-50.2177	-16.3533	-7.3624
17	8.6727	-0.828	2.6861	6.5739	0.4114	7.2165	-0.0816	-0.2956	-0.0732	0.546	0.0789	0.2364	-0.6279	-0.7619	-0.1811	0.7917	-0.0406	0.2026	0.6638	-0.1482	0.8638	-67.696	-8.1324	-2.7794
18	4.1422	-0.0895	-0.6722	5.7117	2.826	2.0181	-0.1869	-0.1279	0.2914	0.5404	-0.6837	2.0987	0.2533	-0.9639	0.6724	0.738	-0.1181	0.0058	0.8306	0.1378	1.455	-78.2553	-15.8938	-10.4377
19	1.7363	0.2253	0.4011	7.6098	-0.9071	8.7235	0.2461	1.2094	0.9627	-1.5495	0.1536	-0.51	-1.2339	-0.5864	-0.4016	0.8958	0.0567	-0.1041	0.7543	0.28	0.9653	-66.7111	-10.0762	-25.3421
20	5.4934	-2.4259	-0.3876	1.1392	0.1954	0.0377	-1.5537	-1.0444	1.7505	-0.5908	2.0888	-0.0768	0.0789	0.654	-1.4639	1.1839	0.1505	0.4806	0.8006	0.0959	1.4713	-57.1715	-0.5878	-19.8872
21	4.0878	1.1701	-0.6186	8.9054	1.5796	2.2386	-0.1629	0.1101	0.8165	0.0479	0.7813	-0.049	-0.1431	0.2983	-0.5649	0.6099	-0.034	0.0885	0.5646	0.0426	0.5604	-59.1272	-19.5929	-16.0114
22	6.0906	1.053	-1.3616	9.1117	-2.6378	2.9445	-0.1128	0.5051	0.4553	-0.0697	0.3798	1.3286	-0.0587	-0.4467	-0.2482	0.5331	-0.0804	-0.0027	0.5704	0.0167	0.5185	-68.9061	-22.5181	-14.3957
23	6.8712	-1.6688	-2.0409	1.2124	-0.666	8.3822	-1.191	0.454	0.7018	-0.1351	-0.0063	1.1512	-0.6189	-1.0618	1.0239	0.7809	0.2458	0.1081	0.8276	-0.1738	1.5916	-82.7743	-5.3221	-9.8994

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 49 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 75 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 76 through 92 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 93 through 137 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 138 through 144 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 12 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 13 through 18 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 19 through 26 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 27 through 75 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 76 through 92 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 93 through 110 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 111 through 127 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 128 through 141 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1 through 49 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 50 through 141 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 12 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 13 through 26 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 27 through 42 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 43 through 49 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 50 through 75 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 76 through 110 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 111 through 139 )

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-Yorodumi

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi