PDB-8gih: Structure of Hepatitis B Virus Capsid Y132A mutant in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 8gih

Title

Structure of Hepatitis B Virus Capsid Y132A mutant in complex with Compound 24

Components

Capsid protein

Keywords

VIRAL PROTEIN/INHIBITOR / HBV / Capsid Assembly / Core Protein / Viral Protein / Inhibitor Complex / VIRAL PROTEIN-INHIBITOR complex

Function / homology

Function and homology information

microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding
Similarity search - Function

Biological species

Hepatitis B virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Shaffer, P.L.

Funding support

1items

Citation

Journal: Bioorg Med Chem Lett / Year: 2022
Title: Diazepinone HBV capsid assembly modulators.
Authors: Kuduk, S.D. / DeRatt, L.G. / Stoops, B. / Shaffer, P. / Lam, A.M. / Espiritu, C. / Vogel, R. / Lau, V. / Flores, O.A. / Hartman, G.D.

History

Deposition	Mar 14, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gih.cif.gz	333.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8gih.ent.gz	272.3 KB	Display	PDB format
PDBx/mmJSON format	8gih.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gih_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	8gih_full_validation.pdf.gz	2.2 MB	Display
Data in XML	8gih_validation.xml.gz	31.5 KB	Display
Data in CIF	8gih_validation.cif.gz	40.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gi/8gih ftp://data.pdbj.org/pub/pdb/validation_reports/gi/8gih	HTTPS FTP

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Related structure data

Related structure data	5e0iS S: Starting model for refinement
Similar structure data	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: Capsid protein

B: Capsid protein

C: Capsid protein

D: Capsid protein

E: Capsid protein

F: Capsid protein

hetero molecules

111 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Capsid protein

F: Capsid protein

hetero molecules

D: Capsid protein

E: Capsid protein

hetero molecules

B: Capsid protein

C: Capsid protein

hetero molecules

defined by author&software
111 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	151.780, 87.570, 103.260
Angle α, β, γ (deg.)	90.00, 103.48, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Capsid protein / Core antigen / Core protein / HBcAg / p21.5 Mass: 18004.578 Da / Num. of mol.: 6 / Mutation: Y132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis B virus / Gene: C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7R9I1
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-ZMH / (6S,8R)-N-(3-bromo-4-fluorophenyl)-8-fluoro-10-methyl-11-oxo-1,3,4,7,8,9,10,11-octahydro-2H-pyrido[4',3':3,4]pyrazolo[1,5-a][1,4]diazepine-2-carboxamide Mass: 454.269 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₈H₁₈BrF₂N₅O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 58 % / Description: Hexagonal
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM ammonium citrate/citric acid pH 6.5, 9% isopropanol, 9.45% PEG 3350, 9% MPD

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 1, 2016

Radiation

Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.65→50 Å / Num. obs: 38129 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC_1/2: 0.997 / R_merge(I) obs: 0.097 / R_rim(I) all: 0.115 / Net I/σ(I): 10.24

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.65-2.72	3.4	0.539	2.32	2796	0.876	0.64	99.8
2.72-2.79		0.425		2740	0.899	0.504
2.79-2.87		0.345		2660	0.958	0.41
2.87-2.96		0.34		2597	0.937	0.404
2.96-3.06		0.265		2512	0.965	0.314
3.06-3.17		0.229		2443	0.962	0.271
3.17-3.29		0.177		2353	0.98	0.209
3.29-3.42		0.119		2242	0.989	0.141
3.42-3.57		0.123		2190	0.99	0.146
3.57-3.75		0.088		2061	0.995	0.104
3.75-3.95		0.076		1976	0.995	0.09
3.95-4.19		0.064		1879	0.996	0.076
4.19-4.48		0.056		1749	0.996	0.066
4.48-4.84		0.049		1657	0.998	0.058
4.84-5.3		0.052		1475	0.996	0.061
5.3-5.93		0.05		1369	0.997	0.059
5.93-6.84		0.051		1211	0.996	0.061
6.84-8.38		0.039		1002	0.998	0.047
8.38-11.85		0.029		797	0.999	0.035
11.85-50		0.031		420	0.999	0.038

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Processing

Software

Name	Version	Classification
XDS	20151015	data reduction
XSCALE	20151231	data scaling
PHENIX	DEV_2463	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5E0I

5e0i

Resolution: 2.65→36.9 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / Phase error: 28.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.253	2054	5.4 %	Random
R_work	0.205	-	-	-
obs	0.208	38033	99.1 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 58.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→36.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6185	0	180	40	6405

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	6571
X-RAY DIFFRACTION	f_angle_d	0.96	9035
X-RAY DIFFRACTION	f_dihedral_angle_d	15.349	3764
X-RAY DIFFRACTION	f_chiral_restr	0.045	1015
X-RAY DIFFRACTION	f_plane_restr	0.006	1130

LS refinement shell

Resolution: 2.65→2.72 Å

	R_factor	Num. reflection	% reflection
R_free	0.3823	151	6 %
R_work	0.3086	2359	-
obs	-	-	100 %

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	4.5941	1.2034	0.242	3.7549	-1.6431	2.3384	-0.0528	0.0484	-0.2931	0.0499	-0.0476	-0.0354	-0.1405	0.1643	0.1135	0.232	-0.0381	0.0133	0.3501	-0.0749	0.6389	160.3162	-51.1579	128.9876
2	4.8818	2.2416	-2.1628	4.4218	-1.9978	1.4116	0.0641	-1.1049	0.7379	1.7604	-0.1978	1.0153	0.5229	-0.0746	0.1789	1.1325	0.0595	-0.1627	0.7206	-0.2261	0.7241	159.4036	-50.5066	150.0607
3	3.6841	1.3788	-1.0476	2.9321	-0.546	2.2512	-0.0672	0.3682	-0.5533	-0.2351	0.1653	0.1677	0.1411	0.0626	-0.1105	0.2727	0.0617	-0.0386	0.3823	-0.0794	0.7871	144.6485	-51.7815	125.5369
4	5.8439	1.6025	0.0589	4.3965	2.0245	1.9947	0.023	0.0579	0.6494	0.1803	-0.0455	0.3419	0.0886	-0.2169	0.0431	0.2371	-0.0265	0.0445	0.3706	0.0271	0.7276	171.4788	-41.7696	129.3168
5	7.5551	-0.1147	-1.1381	5.0308	0.652	0.2368	0.2813	-0.3991	0.7578	0.5457	-0.2913	0.0899	-0.1169	0.2316	-0.2445	0.2623	-0.1189	-0.003	0.3168	-0.0254	0.6222	176.3508	-42.0084	132.7882
6	9.43	0.5882	3.3414	4.6108	0.947	5.0742	-0.161	0.4233	1.0995	-0.0856	0.1237	-0.3593	-0.5684	0.2172	-0.1316	0.2738	0.0196	0.0835	0.3677	0.0369	0.8032	193.3165	-40.9798	124.7282
7	2.915	-1.2578	1.7828	3.8688	0.0533	1.9933	0.0497	0.0429	0.1639	0.0189	-0.0777	-0.0932	-0.2017	0.0337	0.0083	0.241	0.0089	0.0981	0.3914	-0.0039	0.7706	172.8752	-5.4257	128.543
8	5.3766	-1.5898	2.961	1.7399	-2.799	5.223	-0.0752	-0.6884	-0.334	-0.4368	0.4116	0.0395	2.1811	-0.0222	-0.1988	0.9801	-0.0681	-0.1138	0.8159	0.2182	0.6166	172.6755	-6.4943	146.8944
9	5.0774	-2.5465	1.1816	6.812	-2.1829	2.6304	0.2799	0.3057	1.0957	-0.4312	0.0688	-0.1367	0.3074	-0.3084	-0.2456	0.3013	-0.0027	0.0609	0.3082	-0.073	0.4387	178.1931	-15.728	125.864
10	8.9996	1.188	-1.3225	3.1645	2.1352	1.9819	0.0743	0.1811	0.0719	-0.0247	-0.9332	-1.9938	-0.0521	0.8584	0.7582	0.2622	-0.0063	0.0296	0.4468	-0.0549	0.8068	189.463	-25.6575	126.3905
11	8.2718	-3.4801	-3.0542	4.4714	0.3261	2.0029	0.293	-0.3918	0.491	0.0045	-0.1056	-0.4118	0.0256	0.436	-0.208	0.3249	-0.0105	-0.038	0.368	-0.0313	0.6813	161.4625	10.638	127.935
12	4.9683	-0.2325	-1.9506	2.6708	0.0634	3.0902	-0.0227	0.2188	-0.9796	-0.107	-0.103	0.4633	0.0731	-0.0814	0.0129	0.291	0.0329	-0.047	0.3686	-0.054	1.1163	157.2307	-5.6181	127.932
13	5.5266	-1.5342	-1.3139	5.3469	-1.1178	1.6299	0.0457	0.0735	-0.0192	-0.0704	0.0482	0.7919	0.0767	0.2041	-0.0925	0.248	0.006	-0.0613	0.3581	-0.0333	0.74	154.0588	9.9853	127.0313
14	5.1612	-0.3326	0.3649	0.5633	-0.4005	1.3817	0.4302	0.1694	-0.5086	0.0413	-0.1938	0.6313	0.1661	-0.8465	0.0476	-0.0237	-0.0824	-0.0561	0.5341	-0.048	1.3642	142.261	20.2123	125.7708
15	3.9059	0.8332	-0.6916	7.4487	2.2891	1.354	0.0452	-0.33	0.1158	0.0644	0.2583	-1.4282	0.0339	0.3017	-0.2167	0.3222	-0.023	-0.0493	0.3871	0.0103	0.8478	137.2122	-13.9549	128.3163
16	2.6183	0.5862	-0.3051	9.1558	2.8406	4.4764	0.4106	0.1852	0.1862	-0.5147	-0.729	0.9141	0.2255	-0.9378	0.3353	0.329	0.0103	-0.153	0.317	0.0445	0.8487	117.8976	-16.0725	124.096
17	3.2938	0.7377	2.5108	5.1673	-1.1777	2.6384	-0.2765	-0.3341	-0.1983	0.0514	0.1752	0.0798	-0.5682	-0.4944	-0.028	0.28	0.0789	-0.0427	0.3513	-0.0373	0.8259	124.0986	-21.2096	131.9237
18	3.9543	1.9829	-2.3834	1.1577	-0.3543	5.8626	0.2848	0.2991	-0.5398	1.3071	0.2189	-0.7237	-1.2197	-0.6622	-0.7055	1.0687	0.2802	-0.0703	0.6712	-0.1139	0.8492	130.1951	-16.2049	147.3127
19	4.1013	0.6618	-0.6303	4.6635	0.896	5.5658	0.1457	0.2888	0.2204	-0.2203	0.2335	0.4863	0.1015	0.0893	-0.3937	0.2464	-0.0147	-0.0514	0.3474	0.1388	0.7959	132.9526	-7.2669	125.5556
20	3.0114	-0.0012	-0.8113	4.5058	0.843	2.1698	-0.7555	-0.1229	1.2413	-0.5724	-0.0474	1.0534	-0.8175	-0.335	0.6004	0.272	0.1106	0.011	0.4058	0.0069	1.0247	136.08	7.2312	125.8019
21	1.7884	0.1595	1.6197	5.9341	-1.6493	1.9428	0.0325	-0.2161	-0.1256	0.1442	0.1778	1.0675	-0.2201	-0.161	-0.221	0.2746	0.0057	0.0491	0.3627	-0.0071	0.8227	118.704	-35.0868	128.5615
22	1.9728	-0.8068	1.1956	7.1868	-1.2332	2.9822	-0.015	-0.071	0.1131	-0.101	0.0988	-1.0334	-0.1879	0.2338	0.1143	0.1953	0.0297	0.0018	0.3261	-0.0159	0.8319	135.0423	-29.7117	129.8715
23	5.5575	-0.7247	-1.4817	6.6148	-2.1598	1.5446	0.1556	-0.1237	0.2492	-0.1349	0.8231	1.5692	0.4472	0.0286	-0.8229	1.0509	0.3661	0.0708	0.9582	0.328	0.6243	126.1965	-32.7934	147.966
24	2.443	2.2559	0.7329	7.6035	-0.1872	2.1965	0.1989	0.2221	-0.6089	-0.2058	-0.1135	-0.1958	-0.1615	-0.0839	-0.1001	0.2646	0.0044	0.0452	0.3379	-0.0873	0.7469	122.7787	-41.7566	125.8923
25	1.6374	-1.7172	0.9207	8.83	0.5538	0.8594	-0.3791	-0.4026	-0.621	-1.0616	-0.2387	-1	0.4728	0.6421	0.294	0.3278	0.1376	-0.0847	0.3817	-0.0568	1.0949	119.7744	-56.4441	126.4371

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain A and resseq 0:75	A	A	0 - 75	0 - 75
2	2	chain A and resseq 76:92	A	A	76 - 92	76 - 92
3	3	chain A and resseq 93:142	A	A	93 - 142	93 - 142
4	4	chain B and resseq 0:75	B	B	0 - 75	0 - 75
5	5	chain B and resseq 76:110	B	B	76 - 110	76 - 110
6	6	chain B and resseq 111:141	B	B	111 - 141	111 - 141
7	7	chain C and resseq 0:72	C	C	0 - 72	0 - 72
8	8	chain C and resseq 73:92	C	C	73 - 92	73 - 92
9	9	chain C and resseq 93:127	C	C	93 - 127	93 - 127
10	10	chain C and resseq 128:142	C	C	128 - 142	128 - 142
11	11	chain D and resseq 0:26	D	D	0 - 26	0 - 26
12	12	chain D and resseq 27:86	D	D	27 - 86	27 - 86
13	13	chain D and resseq 87:127	D	D	87 - 127	87 - 127
14	14	chain D and resseq 128:142	D	D	128 - 142	128 - 142
15	15	chain E and resseq 0:26	E	E	0 - 26	0 - 26
16	16	chain E and resseq 27:49	E	E	27 - 49	27 - 49
17	17	chain E and resseq 50:70	E	E	50 - 70	50 - 70
18	18	chain E and resseq 71:92	E	E	71 - 92	71 - 92
19	19	chain E and resseq 93:127	E	E	93 - 127	93 - 127
20	20	chain E and resseq 128:142	E	E	128 - 142	128 - 142
21	21	chain F and resseq 0:26	F	F	0 - 26	0 - 26
22	22	chain F and resseq 27:75	F	F	27 - 75	27 - 75
23	23	chain F and resseq 76:92	F	F	76 - 92	76 - 92
24	24	chain F and resseq 93:127	F	F	93 - 127	93 - 127
25	25	chain F and resseq 128:142	F	F	128 - 142	128 - 142

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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