PDB-4p12: Native Structure of the P domain from a GI.7 Norovirus variant.

ID or keywords:

Entry

Database: PDB / ID: 4p12

Title

Native Structure of the P domain from a GI.7 Norovirus variant.

Components

Major capsid protein

Keywords

VIRAL PROTEIN / P domain /

Capsid protein /

Norovirus /

HBGA

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 /

Viral coat protein subunit /

Beta Barrel / Mainly Beta
Similarity search - Domain/homology

Biological species

Norovirus Hu/GI.7/TCH-060/USA/2003

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6011 Å

Authors

Shanker, S. / Czako, R. / Sankaran, B. / Atmar, R. / Estes, M. / Prasad, B.V.V.

Funding support

United States, 2items

Citation

Journal: J.Virol. / Year: 2014
Title: Structural analysis of determinants of histo-blood group antigen binding specificity in genogroup I noroviruses.
Authors: Shanker, S. / Czako, R. / Sankaran, B. / Atmar, R.L. / Estes, M.K. / Prasad, B.V.

History

Deposition	Feb 24, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 2, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 21, 2014	Group: Database references
Revision 1.2	Sep 6, 2017	Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_symm_contact Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.3	Nov 1, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4	Nov 20, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 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 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4p12.cif.gz	471.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4p12.ent.gz	387.2 KB	Display	PDB format
PDBx/mmJSON format	4p12.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p1/4p12 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/4p12	HTTPS FTP

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Related structure data

Related structure data	4p1vC 4p25C 4p26C 4p2nC 4p3iC 2zl5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4p2n-2 4p1v-1 4p3i-2 4p3i-1 4p1v-2 4p25-1 2zl7-d 4p2n-1 4p25-2 5n7m-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 - HomologyF&H Search

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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: Major capsid protein

B: Major capsid protein

C: Major capsid protein

D: Major capsid protein

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

1

A: Major capsid protein

D: Major capsid protein

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

2

B: Major capsid protein

C: Major capsid protein

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

Unit cell

Length a, b, c (Å)	62.181, 63.179, 90.470
Angle α, β, γ (deg.)	99.51, 97.89, 119.17
Int Tables number	1
Space group name H-M	P1

Details

Gel filtration shows dimer

#1: Protein	Major capsid protein Mass: 32617.451 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus Hu/GI.7/TCH-060/USA/2003 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8FL04
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1418 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Sodium Formate, 0.1M Bis Tris Propane, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97935 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97935 Å / Relative weight: 1
Reflection	Resolution: 1.6→40 Å / Num. obs: 146576 / % possible obs: 97.1 % / Redundancy: 3.9 % / R_merge(I) obs: 0.096 / Net I/σ(I): 14.1
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / % possible all: 95.3

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZL5

2zl5

Resolution: 1.6011→39.018 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1817	7189	5.02 %	Random
R_work	0.1555	-	-	-
obs	0.1568	143078	94.68 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6011→39.018 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8888	0	0	1418	10306

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	9184
X-RAY DIFFRACTION	f_angle_d	1.241	12576
X-RAY DIFFRACTION	f_dihedral_angle_d	12.223	3287
X-RAY DIFFRACTION	f_chiral_restr	0.082	1392
X-RAY DIFFRACTION	f_plane_restr	0.007	1678

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 (%)
1.6011-1.6193	0.267	130	0.2085	2703	X-RAY DIFFRACTION	55
1.6193-1.6384	0.2688	181	0.203	3503	X-RAY DIFFRACTION	74
1.6384-1.6584	0.246	222	0.1953	4201	X-RAY DIFFRACTION	88
1.6584-1.6794	0.2278	242	0.187	4496	X-RAY DIFFRACTION	93
1.6794-1.7015	0.2047	225	0.181	4524	X-RAY DIFFRACTION	95
1.7015-1.7248	0.2328	256	0.1779	4569	X-RAY DIFFRACTION	95
1.7248-1.7494	0.2126	230	0.1767	4561	X-RAY DIFFRACTION	96
1.7494-1.7755	0.2241	222	0.1718	4674	X-RAY DIFFRACTION	96
1.7755-1.8033	0.1921	256	0.1658	4569	X-RAY DIFFRACTION	96
1.8033-1.8328	0.1915	246	0.1624	4596	X-RAY DIFFRACTION	96
1.8328-1.8644	0.1884	236	0.1549	4621	X-RAY DIFFRACTION	97
1.8644-1.8983	0.1638	234	0.1545	4598	X-RAY DIFFRACTION	96
1.8983-1.9348	0.1744	240	0.1586	4646	X-RAY DIFFRACTION	97
1.9348-1.9743	0.1983	244	0.1551	4666	X-RAY DIFFRACTION	97
1.9743-2.0173	0.1807	245	0.1525	4564	X-RAY DIFFRACTION	97
2.0173-2.0642	0.171	247	0.1505	4649	X-RAY DIFFRACTION	97
2.0642-2.1158	0.1763	246	0.1506	4693	X-RAY DIFFRACTION	97
2.1158-2.173	0.1719	277	0.1494	4590	X-RAY DIFFRACTION	97
2.173-2.2369	0.1885	250	0.1438	4654	X-RAY DIFFRACTION	98
2.2369-2.3091	0.1722	250	0.152	4684	X-RAY DIFFRACTION	98
2.3091-2.3917	0.1831	245	0.1569	4681	X-RAY DIFFRACTION	98
2.3917-2.4874	0.2042	230	0.1641	4679	X-RAY DIFFRACTION	98
2.4874-2.6006	0.19	263	0.1675	4695	X-RAY DIFFRACTION	98
2.6006-2.7377	0.2007	234	0.1678	4725	X-RAY DIFFRACTION	98
2.7377-2.9091	0.1988	257	0.1659	4714	X-RAY DIFFRACTION	98
2.9091-3.1337	0.19	276	0.1574	4681	X-RAY DIFFRACTION	99
3.1337-3.4488	0.1648	266	0.142	4677	X-RAY DIFFRACTION	99
3.4488-3.9475	0.153	266	0.1371	4757	X-RAY DIFFRACTION	99
3.9475-4.9718	0.1381	252	0.1267	4711	X-RAY DIFFRACTION	99
4.9718-39.03	0.1941	221	0.1701	4808	X-RAY DIFFRACTION	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	1.4624	-0.1707	-0.0164	0.7045	-0.0174	0.9733	-0.0093	-0.081	0.0544	0.0737	0.0164	-0.0272	-0.0109	0.0967	0.0102	0.0816	-0.0266	-0.0064	0.0758	-0.003	0.0555	29.7204	14.1078	61.2547
2	1.4783	-0.1798	-0.1831	1.3642	0.0957	1.4486	-0.0312	-0.149	-0.0752	0.048	0.0187	-0.1268	0.0934	0.1907	0.042	0.0672	0.0043	-0.0221	0.095	0.0088	0.0844	41.1985	4.2641	57.6365
3	1.2135	-0.1887	-0.2915	0.9109	0.1007	0.6726	-0.0328	-0.1337	-0.0826	0.1147	0.0324	-0.0035	0.0339	0.0484	-0.0182	0.0745	-0.0167	-0.0021	0.0707	0.0118	0.0632	23.2315	9.7041	62.3504
4	2.2136	0.2347	0.3134	2.3071	0.4111	2.3332	0.0368	0.0194	0.1109	0.0458	-0.0197	0.2032	-0.1539	-0.2178	0.035	0.0714	0.0042	0.0304	0.0835	0.0078	0.1161	9.044	19.8342	59.2042
5	2.8397	0.3646	-1.2381	3.1068	1.0123	3.6228	0.0332	-0.0472	-0.0342	0.1507	0.0181	0.2725	0.0191	-0.2558	-0.0238	0.0689	0.0156	-0.0185	0.0951	0.0222	0.1115	6.6143	18.1962	58.7934
6	1.5852	0.1517	0.1664	1.2533	0.0308	1.039	-0.0078	0.0268	-0.0402	-0.0928	0.0004	-0.0983	0.0276	0.0612	0.0408	0.0757	0.0134	0.001	0.0732	-0.0089	0.0762	9.8115	-28.1114	92.2961
7	2.2893	0.5724	0.2177	0.9729	-0.129	0.2463	0.0038	0.0104	-0.155	-0.0712	0.0638	0.3514	0.0355	-0.258	0.068	0.1158	0.0027	-0.0319	0.1419	-0.0027	0.139	-15.5069	-30.6	90.3863
8	2.1169	0.0577	-0.4837	1.0243	0.2244	1.8118	-0.0058	0.0582	-0.0264	-0.0326	-0.0663	0.2018	0.0101	-0.273	0.0368	0.0623	0.0005	-0.0192	0.1168	-0.0026	0.0939	-13.8744	-30.1279	99.0183
9	1.7085	0.1445	-0.3512	0.4932	0.1722	0.842	-0.0435	-0.0669	-0.2028	-0.0102	0.0298	-0.0388	0.1309	0.0016	-0.0259	0.0846	0.0103	-0.0114	0.0623	-0.0031	0.087	4.3819	-33.3232	98.024
10	2.0727	-0.3813	-0.0584	2.0321	0.6102	2.7786	0.0003	-0.109	0.0012	-0.07	0.0278	-0.2511	0.0613	0.2785	-0.051	0.0838	0.0227	0.0218	0.1094	-0.0018	0.1263	23.8544	-28.0987	93.3212
11	0.5113	-0.157	0.2564	0.6502	-0.4675	1.4741	0.0197	-0.011	0.0228	-0.0931	-0.0287	0.0035	0.0536	-0.0182	0.0161	0.0813	0.0062	-0.0051	0.0597	-0.0114	0.0612	0.9756	-7.8854	97.7617
12	0.6447	0.1132	-0.3878	0.6835	-0.5634	1.5054	0.0163	-0.0573	0.0298	0.0252	-0.0044	0.054	-0.0851	-0.074	0.01	0.07	0.0089	-0.0121	0.0747	-0.0179	0.0627	-4.7454	-7.1684	102.6134
13	1.2036	0.0998	-0.4308	1.2328	-0.2635	1.6138	0.0513	0.143	0.0698	-0.2287	-0.0997	0.0146	0.0144	-0.0585	0.0257	0.1577	0.0476	-0.0044	0.098	0.0154	0.0643	0.8596	-3.9579	75.2772
14	0.6539	0.4447	0.2868	0.9979	0.4899	0.9935	0.0203	0.031	0.0431	-0.0016	0.0062	-0.0441	-0.0484	0.039	-0.0076	0.0544	-0.0139	0.0064	0.0623	0.0097	0.0716	33.7157	24.3662	42.0665
15	1.4928	-0.3913	-0.0164	1.7272	-0.2262	1.1646	0.0214	0.1029	-0.0577	-0.0916	-0.037	-0.0476	0.046	0.0667	0.0018	0.0552	-0.0092	0.0023	0.0697	-0.0178	0.0592	37.1068	11.5574	34.7889
16	1.0061	-0.5005	0.1151	1.0289	0.3704	1.6326	0.0846	0.0524	0.0902	-0.0366	-0.0379	-0.2725	-0.0003	0.2005	0.0247	0.0641	0.0076	0.0109	0.0787	-0.0008	0.1201	45.3563	15.7842	38.1211
17	3.1071	-0.1425	0.103	3.792	-0.0567	1.2055	-0.0673	0.6594	0.2136	-0.5613	0.056	0.4012	-0.24	0.0049	-0.0395	0.1975	-0.0319	-0.0038	0.2039	0.0448	0.1554	36.0164	29.7199	30.3612
18	0.7797	0.2406	0.1669	2.9567	-0.3836	0.9979	-0.0103	0.0751	0.1509	-0.2155	0.0625	-0.2575	-0.1196	0.1569	0.0124	0.0994	-0.0463	0.0089	0.0907	-0.0059	0.1291	45.0464	32.8515	45.689
19	0.5414	0.75	0.0181	1.2414	0.5355	1.3188	-0.0172	-0.0272	0.1936	0.0888	-0.0403	0.1998	-0.0597	-0.095	0.0437	0.1106	-0.0255	0.0067	0.0745	-0.024	0.1369	30.9337	35.9398	51.7219
20	1.0396	0.2327	-0.0186	1.1279	-0.1139	1.075	-0.0677	-0.0693	0.1127	0.066	0.0402	-0.0387	-0.1615	0.0451	0.0641	0.1035	-0.0245	0.0091	0.0687	-0.021	0.1506	40.1088	41.6201	55.8231
21	4.3634	-0.7091	0.4019	3.5972	-0.5929	0.2691	0.0096	0.0123	0.3053	0.011	-0.0821	-0.134	-0.0734	0.0969	0.0529	0.1303	-0.0384	0.0048	0.0915	-0.0488	0.0955	38.8026	43.6557	55.6088

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 229 through 317 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 318 through 397 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 398 through 458 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 459 through 500 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 501 through 526 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 226 through 289 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 290 through 319 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 320 through 377 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 378 through 458 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 459 through 526 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 232 through 317 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 318 through 458 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 459 through 526 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 232 through 317 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 318 through 377 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 378 through 397 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 398 through 417 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 418 through 441 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 442 through 473 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 474 through 500 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 501 through 526 )

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