PDB-5kou: Crystal structure of the human astrovirus 2 capsid protein spike ...

ID or keywords:

Entry

Database: PDB / ID: 5kou

Title

Crystal structure of the human astrovirus 2 capsid protein spike domain at 1.87-A resolution

Components

Capsid polyprotein VP25

Keywords

VIRAL PROTEIN / capsid protein / icosahedral virus.

Function / homology

Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / Capsid polyprotein VP90

Function and homology information

Biological species

Human astrovirus-2

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.867 Å

Authors

Bogdanoff, W.A. / DuBois, R.M.

Funding support

United States, 1items

Citation

Journal: J. Virol. / Year: 2017
Title: Structure of a Human Astrovirus Capsid-Antibody Complex and Mechanistic Insights into Virus Neutralization.
Authors: Bogdanoff, W.A. / Campos, J. / Perez, E.I. / Yin, L. / Alexander, D.L. / DuBois, R.M.

History

Deposition	Jul 1, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2016	Group: Database references
Revision 1.2	Jan 18, 2017	Group: Database references
Revision 1.3	Sep 6, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Nov 1, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Oct 4, 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

-
Download

PDBx/mmCIF format	5kou.cif.gz	366.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5kou.ent.gz	301.9 KB	Display	PDB format
PDBx/mmJSON format	5kou.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/5kou ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5kou	HTTPS FTP

-
Related structure data

Related structure data	5kovC 3qsqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5w1n-2 7lbh-d 6ni7-d 7l9q-d 4qgs-d 6ni6-d 2v32-1 4au9-2 7l9w-d 7ldb-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Capsid polyprotein VP25

B: Capsid polyprotein VP25

C: Capsid polyprotein VP25

D: Capsid polyprotein VP25

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

1

A: Capsid polyprotein VP25

B: Capsid polyprotein VP25

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

2

C: Capsid polyprotein VP25

D: Capsid polyprotein VP25

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

Unit cell

Length a, b, c (Å)	44.070, 67.720, 90.530
Angle α, β, γ (deg.)	76.53, 80.52, 86.29
Int Tables number	1
Space group name H-M	P1

Details

Dimer confirmed by gel filtration

#1: Protein	Capsid polyprotein VP25 Mass: 27660.322 Da / Num. of mol.: 4 / Fragment: UNP Residues 429-644 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human astrovirus-2 / Gene: ORF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q82446
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.32 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, sodium citrate, ammonium sulfate

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 1.033202 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 18, 2014

Radiation

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

Radiation wavelength

Wavelength: 1.033202 Å / Relative weight: 1

Reflection

Resolution: 1.867→47.58 Å / Num. obs: 80310 / % possible obs: 96.3 % / Redundancy: 2 % / B_iso Wilson estimate: 20.38 Å² / CC_1/2: 0.987 / R_merge(I) obs: 0.073 / R_sym value: 0.073 / Net I/σ(I): 7.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.867-1.97	2	0.445	1	93.6
5.9-47.58	1.9	0.035	1	94.4

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10_2152: ???)	refinement
iMOSFLM	7.1.1	data reduction
SCALA	3.3.21	data scaling
PHASER	6.5.0	phasing
Coot	0.8.2	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3QSQ

3qsq

Resolution: 1.867→47.578 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2149	3985	4.96 %	RANDOM
R_work	0.1932	-	-	-
obs	0.1943	80278	96.28 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.867→47.578 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7059	0	0	335	7394

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7326
X-RAY DIFFRACTION	f_angle_d	0.706	10002
X-RAY DIFFRACTION	f_dihedral_angle_d	13.638	4397
X-RAY DIFFRACTION	f_chiral_restr	0.049	1118
X-RAY DIFFRACTION	f_plane_restr	0.005	1276

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 (%)
1.867-1.8898	0.3697	113	0.3194	2530	X-RAY DIFFRACTION	88
1.8898-1.9137	0.3499	135	0.2934	2745	X-RAY DIFFRACTION	95
1.9137-1.9389	0.3097	142	0.2694	2652	X-RAY DIFFRACTION	95
1.9389-1.9654	0.2662	147	0.2538	2649	X-RAY DIFFRACTION	95
1.9654-1.9935	0.2261	157	0.25	2771	X-RAY DIFFRACTION	96
1.9935-2.0233	0.2767	134	0.2448	2662	X-RAY DIFFRACTION	96
2.0233-2.0549	0.2587	147	0.2311	2728	X-RAY DIFFRACTION	96
2.0549-2.0886	0.2591	146	0.2356	2698	X-RAY DIFFRACTION	96
2.0886-2.1246	0.2775	157	0.2298	2700	X-RAY DIFFRACTION	96
2.1246-2.1632	0.2634	133	0.2268	2693	X-RAY DIFFRACTION	96
2.1632-2.2048	0.2394	151	0.2244	2754	X-RAY DIFFRACTION	96
2.2048-2.2498	0.2516	137	0.2123	2723	X-RAY DIFFRACTION	96
2.2498-2.2988	0.2655	131	0.2165	2720	X-RAY DIFFRACTION	96
2.2988-2.3522	0.2471	143	0.2117	2715	X-RAY DIFFRACTION	97
2.3522-2.4111	0.2207	138	0.2173	2749	X-RAY DIFFRACTION	97
2.4111-2.4762	0.2243	128	0.212	2742	X-RAY DIFFRACTION	97
2.4762-2.5491	0.2664	159	0.215	2709	X-RAY DIFFRACTION	97
2.5491-2.6314	0.2426	152	0.2131	2788	X-RAY DIFFRACTION	97
2.6314-2.7254	0.2405	154	0.212	2725	X-RAY DIFFRACTION	97
2.7254-2.8345	0.2565	146	0.2027	2752	X-RAY DIFFRACTION	97
2.8345-2.9635	0.2038	130	0.1941	2774	X-RAY DIFFRACTION	97
2.9635-3.1197	0.209	133	0.1911	2771	X-RAY DIFFRACTION	98
3.1197-3.3151	0.1919	147	0.1766	2746	X-RAY DIFFRACTION	98
3.3151-3.571	0.1912	148	0.1691	2779	X-RAY DIFFRACTION	98
3.571-3.9302	0.1827	133	0.1562	2793	X-RAY DIFFRACTION	98
3.9302-4.4986	0.1622	146	0.1409	2777	X-RAY DIFFRACTION	98
4.4986-5.6663	0.1378	145	0.1431	2779	X-RAY DIFFRACTION	98
5.6663-47.5931	0.181	153	0.1741	2669	X-RAY DIFFRACTION	95

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	4.0129	1.4635	-5.1256	1.9387	-0.7849	7.3931	-0.3826	0.2824	-0.0383	0.0409	0.0481	0.4238	0.2559	-0.256	0.19	0.2288	-0.0186	-0.0389	0.2276	0.0099	0.1446	-10.6499	-7.2647	25.1968
2	1.9959	-0.3075	-0.2086	1.144	-0.0598	2.8001	-0.1113	0.1173	-0.305	-0.0529	-0.0567	-0.2044	0.9432	0.4614	0.0622	0.3177	0.0539	0.0271	0.1821	0.0033	0.2051	4.6163	-16.279	6.8682
3	0.8972	0.0004	-0.6287	1.9801	-0.7954	2.7815	-0.0591	0.0054	-0.174	0.0286	-0.0174	-0.0037	0.3783	-0.0464	0.0621	0.1468	-0.0329	-0.0221	0.1365	-0.0389	0.1426	-4.5777	-14.3894	11.6687
4	0.9939	-0.0436	-0.3089	2.5112	-0.4897	2.6245	0.0143	0.1136	-0.0982	-0.0541	-0.0145	0.2167	0.2776	-0.4361	0.0012	0.1558	-0.0316	0.0059	0.1963	-0.0222	0.1252	-7.9934	-10.5604	9.5389
5	2.207	0.2633	-1.3399	2.1876	-1.1397	3.7775	0.1139	0.1358	0.1828	-0.0603	-0.0277	-0.0718	-0.3809	-0.0002	-0.0877	0.1123	0.0134	-0.0098	0.1236	-0.0117	0.1289	-5.5269	14.6185	6.2578
6	2.0819	-0.6606	0.0732	2.3943	-0.1793	2.2023	0.0475	-0.0526	0.2253	0.2658	-0.0077	-0.1399	-0.2301	0.1355	-0.0426	0.1373	-0.0372	-0.0192	0.1399	-0.0248	0.1149	-3.1863	17.031	17.298
7	1.2747	-0.5254	-0.5946	1.5432	0.1767	1.4277	0.0362	0.036	0.0663	-0.0615	-0.0527	-0.1652	-0.0778	0.0884	0.0134	0.1045	-0.0073	-0.0168	0.1534	0.0089	0.1168	1.4319	9.8141	6.0756
8	4.9828	3.3623	-0.6655	6.104	-0.1709	2.5292	0.3783	-0.6317	0.0306	1.1676	-0.1067	-0.9805	-0.554	0.5487	-0.1773	0.3895	-0.1003	-0.1174	0.4245	-0.0126	0.4063	1.3661	14.8604	25.3626
9	1.6087	-0.3603	0.2213	2.9078	-0.7728	3.8764	-0.0991	-0.1847	-0.1909	-0.1436	0.1712	0.5223	0.3278	-0.1007	-0.0946	0.1487	-0.0054	0.0213	0.1463	0.0431	0.2726	-29.5433	19.1851	-19.5005
10	1.137	0.2679	0.2614	4.0976	0.3987	2.0294	-0.1176	0.0175	-0.2265	-0.4832	0.1407	0.1493	0.0775	0.0015	-0.0289	0.1705	0.001	-0.0051	0.1327	0.0227	0.1745	-23.4211	18.433	-23.7966
11	2.9097	-0.0252	1.9356	3.0665	-0.095	7.2799	-0.1664	0.0236	-0.05	-0.2464	0.1148	-1.3292	-0.0677	1.1073	0.0743	0.2497	0.027	0.0746	0.3261	-0.0479	0.4777	-8.6997	14.1955	-26.4501
12	2.7773	-0.3269	0.6555	3.2577	0.0431	2.3502	-0.035	0.0511	-0.1322	-0.3486	0.0579	0.0622	-0.0286	0.079	-0.0175	0.1724	-0.0055	0.0133	0.124	-0.0055	0.1284	-20.944	24.8569	-22.545
13	1.3174	-0.7773	-0.8546	3.368	-0.0092	2.3005	-0.0012	-0.0798	0.1691	-0.2775	0.1117	-0.5432	-0.23	0.1274	-0.0579	0.1636	-0.0111	-0.0075	0.1277	-0.031	0.1795	-16.0605	45.0647	-20.8337
14	1.807	-0.3161	0.1382	1.7489	-0.4199	2.5055	-0.0384	0.117	0.2997	-0.7085	0.035	-0.1907	-0.0287	-0.1147	0.0202	0.3595	-0.0465	0.0004	0.1428	0.0152	0.1575	-21.6219	50.9857	-31.3844
15	3.0293	1.2494	0.7503	4.1997	0.7197	1.4238	0.0992	-0.2706	0.1015	-0.2916	-0.1801	0.4136	-0.0624	-0.0997	0.0521	0.2087	0.0249	-0.0682	0.1688	-0.0173	0.21	-29.2719	48.8208	-24.528
16	1.5138	0.1013	-0.2979	3.9968	-0.4961	1.7487	-0.0519	-0.0702	-0.0166	-0.0808	0.0713	0.0662	-0.0543	-0.0441	-0.0047	0.1338	0.0166	-0.0174	0.1256	-0.0232	0.1057	-22.9583	44.5645	-19.2813

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 430:434)
2	X-RAY DIFFRACTION	2	(chain A and resid 435:467)
3	X-RAY DIFFRACTION	3	(chain A and resid 468:586)
4	X-RAY DIFFRACTION	4	(chain A and resid 587:645)
5	X-RAY DIFFRACTION	5	(chain B and resid 430:467)
6	X-RAY DIFFRACTION	6	(chain B and resid 468:553)
7	X-RAY DIFFRACTION	7	(chain B and resid 554:637)
8	X-RAY DIFFRACTION	8	(chain B and resid 638:654)
9	X-RAY DIFFRACTION	9	(chain C and resid 430:466)
10	X-RAY DIFFRACTION	10	(chain C and resid 467:600)
11	X-RAY DIFFRACTION	11	(chain C and resid 601:609)
12	X-RAY DIFFRACTION	12	(chain C and resid 610:648)
13	X-RAY DIFFRACTION	13	(chain D and resid 430:462)
14	X-RAY DIFFRACTION	14	(chain D and resid 463:512)
15	X-RAY DIFFRACTION	15	(chain D and resid 513:536)
16	X-RAY DIFFRACTION	16	(chain D and resid 537:646)

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
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

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-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

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
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

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi