PDB-4rpb: Crystal Structure of P Domain of Snow Mountain Norovirus

ID or keywords:

Entry

Database: PDB / ID: 4rpb

Title

Crystal Structure of P Domain of Snow Mountain Norovirus

Components

Capsid protein VP1

Keywords

VIRAL PROTEIN / Virus internalization /

HBGA / Virus Surface

Function / homology

Function and homology information

Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein /

Viral coat protein subunit ...
Similarity search - Domain/homology

Biological species

NOROVIRUS HU/GII.2/KL109/1978/MYS

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.61 Å

Authors

Singh, B.K. / Hansman, G.S.

Citation

Journal: Msphere / Year: 2016
Title: Structural Constraints on Human Norovirus Binding to Histo-Blood Group Antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.

History

Deposition	Oct 30, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 22, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 29, 2016	Group: Database references
Revision 2.0	Aug 24, 2022	Group: Atomic model / Database references / Derived calculations Category: atom_site / citation ...atom_site / citation / database_2 / struct_ref_seq_dif / struct_site Item: _atom_site.occupancy / _citation.journal_abbrev ..._atom_site.occupancy / _citation.journal_abbrev / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1	Feb 28, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4rpb.cif.gz	506.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4rpb.ent.gz	426.2 KB	Display	PDB format
PDBx/mmJSON format	4rpb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rp/4rpb ftp://data.pdbj.org/pub/pdb/validation_reports/rp/4rpb	HTTPS FTP

-
Related structure data

Related structure data	4roxC 4rpdC C: citing same article (ref.)
Similar structure data	3pa2-2 3onu-2 3ony-5 3ony-4 3pa1-3 3ony-3 2obs-d 3pa1-2 3x1z-d 4i1s-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (4)

Deposited unit

A: Capsid protein VP1

B: Capsid protein VP1

C: Capsid protein VP1

hetero molecules

102 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Capsid protein VP1

hetero molecules

defined by author&software
34.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Capsid protein VP1

hetero molecules

defined by author&software
34.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Capsid protein VP1

hetero molecules

defined by author&software
34.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	166.640, 96.170, 64.120
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-848- HOH

#1: Protein	Capsid protein VP1 / Mass: 34011.113 Da / Num. of mol.: 3 / Fragment: P Domain residues 225-532 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NOROVIRUS HU/GII.2/KL109/1978/MYS / Gene: VP1 / Plasmid: MBP-HTSHP / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: K7X601
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.52 Å³/Da / Density % sol: 51.12 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% w/v PEG 2000, 0.1 M Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979675
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2014
Radiation	Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979675 Å / Relative weight: 1
Reflection	Resolution: 1.6→41.66 Å / Num. obs: 254153 / % possible obs: 96.6 % / Observed criterion σ(I): -3
Reflection shell	Resolution: 1.6→1.64 Å / R_merge(I) obs: 0.644 / Mean I/σ(I) obs: 1.47 / % possible all: 89.9

-
Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	'(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.61→41.66 Å / SU ML: 0.16 / σ(F): 0.82 / Phase error: 19.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1816	12515	5 %
R_work	0.165	-	-
obs	0.1659	250315	97.09 %
all	-	54818	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.61→41.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6860	0	28	690	7578

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7141
X-RAY DIFFRACTION	f_angle_d	1.063	9766
X-RAY DIFFRACTION	f_dihedral_angle_d	12.065	2576
X-RAY DIFFRACTION	f_chiral_restr	0.041	1093
X-RAY DIFFRACTION	f_plane_restr	0.005	1295

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 (%)
1.61-1.6283	0.277	420	0.285	7901	X-RAY DIFFRACTION	96
1.6283-1.6475	0.3018	394	0.2901	7738	X-RAY DIFFRACTION	96
1.6475-1.6675	0.2948	414	0.2807	7769	X-RAY DIFFRACTION	96
1.6675-1.6887	0.2827	419	0.2587	8022	X-RAY DIFFRACTION	96
1.6887-1.7109	0.271	405	0.2489	7757	X-RAY DIFFRACTION	96
1.7109-1.7343	0.2482	421	0.2446	7943	X-RAY DIFFRACTION	97
1.7343-1.7591	0.2413	404	0.2281	7736	X-RAY DIFFRACTION	96
1.7591-1.7853	0.2263	422	0.2136	7998	X-RAY DIFFRACTION	97
1.7853-1.8132	0.2198	421	0.2086	7961	X-RAY DIFFRACTION	97
1.8132-1.843	0.2059	426	0.1988	8066	X-RAY DIFFRACTION	97
1.843-1.8748	0.2028	415	0.1962	7813	X-RAY DIFFRACTION	97
1.8748-1.9088	0.2473	405	0.1934	7774	X-RAY DIFFRACTION	97
1.9088-1.9456	0.1931	423	0.1865	8050	X-RAY DIFFRACTION	97
1.9456-1.9853	0.201	424	0.1682	7955	X-RAY DIFFRACTION	98
1.9853-2.0284	0.1956	422	0.1711	8021	X-RAY DIFFRACTION	98
2.0284-2.0756	0.1976	416	0.1689	7865	X-RAY DIFFRACTION	97
2.0756-2.1275	0.1777	411	0.1591	7985	X-RAY DIFFRACTION	98
2.1275-2.185	0.1713	420	0.1618	8018	X-RAY DIFFRACTION	98
2.185-2.2493	0.1737	412	0.1513	7872	X-RAY DIFFRACTION	97
2.2493-2.3219	0.1835	428	0.1573	8058	X-RAY DIFFRACTION	98
2.3219-2.4049	0.176	424	0.1526	7983	X-RAY DIFFRACTION	98
2.4049-2.5012	0.1724	422	0.157	8007	X-RAY DIFFRACTION	98
2.5012-2.615	0.1777	425	0.1627	8057	X-RAY DIFFRACTION	98
2.615-2.7529	0.1872	423	0.164	8050	X-RAY DIFFRACTION	98
2.7529-2.9253	0.1611	428	0.1541	8093	X-RAY DIFFRACTION	99
2.9253-3.1511	0.1866	424	0.1525	8008	X-RAY DIFFRACTION	99
3.1511-3.468	0.1658	421	0.1563	8046	X-RAY DIFFRACTION	98
3.468-3.9695	0.1846	429	0.1579	8138	X-RAY DIFFRACTION	99
3.9695-4.9999	0.1267	412	0.1218	7830	X-RAY DIFFRACTION	96
4.9999-41.6739	0.1578	385	0.1542	7286	X-RAY DIFFRACTION	90

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	1.08	-0.3184	0.1383	1.9528	0.4413	2.2763	0.0429	0.0415	-0.0055	-0.1823	-0.0266	0.0352	0.0512	0.0184	-0.0113	0.2702	-0.0649	-0.0043	0.0965	0.0064	0.1936	40.0504	-8.0571	11.2008
2	0.5966	0.5336	0.2084	1.4553	-0.1783	1.6422	0.0812	-0.0596	-0.2342	0.0413	-0.0101	0.0094	0.6242	0.048	-0.0604	0.4161	-0.0214	0.0089	0.1141	0.0068	0.2559	45.5449	-22.9286	16.7075
3	0.9887	0.3734	-0.1555	1.4881	0.9721	1.2073	0.0566	0.0595	-0.2039	-0.2829	-0.0084	-0.0758	0.6201	0.3962	-0.0898	0.4583	-0.0086	0.0073	0.0994	-0.0075	0.2255	48.3401	-19.3471	9.169
4	1.1326	0.1209	0.0309	1.8173	0.1713	1.9664	-0.0141	0.1112	0.2099	-0.5537	0.0073	0.2555	-0.4259	-0.1473	-0.0306	0.4589	-0.0347	-0.0595	0.1111	0.0328	0.2449	36.3878	4.8252	5.1931
5	2.299	0.1516	0.7584	1.0613	0.3655	2.5387	0.0335	-0.0885	0.1327	0.0419	-0.0407	-0.0008	-0.1347	0.1171	0.0065	0.2048	-0.1131	0.017	0.1547	-0.0039	0.194	45.1206	-0.9477	31.4855
6	0.7853	0.3731	0.6272	1.1773	0.5721	1.5703	0.0681	-0.1439	0.0177	-0.0086	0.0131	-0.2549	-0.0534	0.7193	-0.0795	0.1734	-0.1234	0.0113	0.3416	0.0002	0.2549	59.5717	-3.9239	28.2471
7	1.4466	0.324	0.2033	1.485	0.1868	1.9804	0.1808	-0.4199	0.1174	0.2439	-0.2088	0.3014	0.085	-0.4532	-0.017	0.225	-0.1658	0.0662	0.3321	-0.0397	0.2421	30.0317	-6.2537	37.5254
8	1.4961	-0.6999	-0.6204	1.9127	0.3778	2.5142	-0.0417	-0.0665	-0.072	0.0618	0.0413	0.1344	-0.0367	-0.175	0.0019	0.0657	0.0403	0.0017	0.2981	0.0132	0.1949	77.5273	19.1437	10.128
9	1.4729	-0.0504	-0.9268	0.4561	0.3025	1.1231	-0.0769	-0.089	0.2239	0.0748	0.1327	0.1406	-0.608	-0.409	-0.1057	0.1956	0.133	0.0022	0.3367	0.008	0.2555	72.886	33.177	6.7994
10	1.7322	-0.2484	-0.1456	1.2689	0.1153	2.0282	-0.1889	-0.4486	-0.3263	0.2231	0.1928	-0.038	0.3632	0.2622	-0.0295	0.1589	0.1307	0.0079	0.3943	0.071	0.2397	89.76	8.8014	16.1598

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 225 through 305 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 306 through 376 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 377 through 416 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 417 through 532 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 225 through 330 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 331 through 416 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 417 through 532 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 225 through 330 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 331 through 416 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 417 through 532 )

-
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://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

-
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

-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

-
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