PDB-4ops: Crystal structure of P domain from norovirus strain Farmington Hi...

ID or keywords:

Entry

Database: PDB / ID: 4ops

Title

Crystal structure of P domain from norovirus strain Farmington Hills 2004 in complex with HBGA type Leb (tetraglycan)

Components

Major capsid protein

Keywords

VIRAL PROTEIN / Norovirus / Viral Capsid Protein / Histo Blood Group Antigen (HBGA) / Protruding Domain

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.4/Farmington Hills/2004/USA

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.76 Å

Authors

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

Citation

Journal: J.Virol. / Year: 2015
Title: Human noroviruses' fondness for histo-blood group antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.

History

Deposition	Feb 6, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 11, 2015	Group: Database references
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Feb 28, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ops.cif.gz	347.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4ops.ent.gz	288.3 KB	Display	PDB format
PDBx/mmJSON format	4ops.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ops_validation.pdf.gz	860.5 KB	Display	wwPDB validaton report
Full document	4ops_full_validation.pdf.gz	860.5 KB	Display
Data in XML	4ops_validation.xml.gz	25 KB	Display
Data in CIF	4ops_validation.cif.gz	37 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/op/4ops ftp://data.pdbj.org/pub/pdb/validation_reports/op/4ops	HTTPS FTP

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Related structure data

Related structure data	4oosC 4oovC 4ooxC 4op7C 4opoC 4wzeC 4wzkC 4wzlC 4wztC 4x05C 4x06C 4x07C 4x0cC C: citing same article (ref.)
Similar structure data	4wzl-d 4wze-d 3skb-2 4z4u-d 5iyr-d 5iyn-d 4wzk-d 3skb-3 4oox-1 5lfe-d 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

hetero molecules

68.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	71.450, 90.110, 91.870
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 225 - 530 / Label seq-ID: 1 - 306

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	chain A	A	A
2	chain B	B	B

#1: Protein

Major capsid protein

Mass: 33699.574 Da / Num. of mol.: 2
Fragment: P domain Farmington Hills 2004 (residues 225 to 530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Norovirus Hu/GII.4/Farmington Hills/2004/USA
Gene: JQ478408 / Plasmid: MBP-HTSHP / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R4I4P2

#2: Polysaccharide

alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2- ... / Lewis B antigen / beta anomer

Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 675.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis B antigen, beta anomer

Descriptor	Type	Program
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3-3/a3-b1_a4-d1_b2-c1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}[(4+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.19 Å³/Da / Density % sol: 43.94 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: PEG 3350, Magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.9794 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 1.75→97.3449 Å / Num. obs: 59028 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / B_iso Wilson estimate: 17.39 Å² / R_merge(I) obs: 0.112 / Net I/σ(I): 9.88

Reflection shell

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.75-1.79		5.7	0.535	2.41	1	95.1
1.79-1.84			0.438	3.22	1	99.8
1.84-1.9			0.707	2.65	1	97.9
1.9-1.95			0.611	3.79	1	83.5
1.95-2.02			0.369	4.94	1	99
2.02-2.09			0.374	5.47	1	97.2
2.09-2.17			0.246	6.95	1	99.4
2.17-2.26			0.219	7.64	1	96.1
2.26-2.36			0.185	8.69	1	98.2
2.36-2.47			0.133	11.17	1	99.7
2.47-2.61			0.119	12.38	1	99.8
2.61-2.76			0.114	13.15	1	99.2
2.76-2.96			0.087	15.3	1	99.4
2.96-3.19			0.078	18.24	1	99.6
3.19-3.5			0.071	19.58	1	98.9
3.5-3.91			0.075	18.88	1	96.7
3.91-4.51			0.058	21.02	1	98
4.51-5.53			0.054	22.83	1	99.2
5.53-7.82			0.055	21.84	1	99.2
	7.82		0.049	22.74	1	97.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.3	phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.14	data extraction
XDS		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.76→47.808 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 21.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2164	2894	5 %
R_work	0.185	-	-
obs	0.1866	57869	97.31 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→47.808 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4723	0	46	324	5093

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	4932
X-RAY DIFFRACTION	f_angle_d	1.362	6746
X-RAY DIFFRACTION	f_dihedral_angle_d	13.333	1770
X-RAY DIFFRACTION	f_chiral_restr	0.058	749
X-RAY DIFFRACTION	f_plane_restr	0.008	894

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	2808	X-RAY DIFFRACTION	4.526	TORSIONAL
1	2	B	2808	X-RAY DIFFRACTION	4.526	TORSIONAL

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 (%)
1.76-1.7889	0.2758	140	0.2068	2653	X-RAY DIFFRACTION	100
1.7889-1.8197	0.2252	139	0.1774	2652	X-RAY DIFFRACTION	100
1.8197-1.8528	0.2453	139	0.1876	2633	X-RAY DIFFRACTION	100
1.8528-1.8884	0.2899	139	0.2593	2636	X-RAY DIFFRACTION	98
1.8884-1.927	0.5335	112	0.5111	2102	X-RAY DIFFRACTION	80
1.927-1.9689	0.3794	124	0.3419	2353	X-RAY DIFFRACTION	89
1.9689-2.0147	0.2197	140	0.1971	2671	X-RAY DIFFRACTION	100
2.0147-2.0651	0.2385	137	0.217	2595	X-RAY DIFFRACTION	98
2.0651-2.1209	0.3173	136	0.2189	2587	X-RAY DIFFRACTION	97
2.1209-2.1833	0.189	140	0.1854	2658	X-RAY DIFFRACTION	100
2.1833-2.2538	0.3098	130	0.256	2522	X-RAY DIFFRACTION	94
2.2538-2.3343	0.2704	138	0.1972	2609	X-RAY DIFFRACTION	97
2.3343-2.4278	0.2024	141	0.1679	2672	X-RAY DIFFRACTION	100
2.4278-2.5383	0.2134	140	0.1706	2664	X-RAY DIFFRACTION	100
2.5383-2.6721	0.203	141	0.1702	2673	X-RAY DIFFRACTION	99
2.6721-2.8395	0.2158	141	0.1677	2684	X-RAY DIFFRACTION	100
2.8395-3.0587	0.1893	141	0.1766	2687	X-RAY DIFFRACTION	99
3.0587-3.3664	0.1991	143	0.177	2705	X-RAY DIFFRACTION	99
3.3664-3.8534	0.1886	140	0.163	2656	X-RAY DIFFRACTION	97
3.8534-4.8541	0.1441	142	0.1326	2707	X-RAY DIFFRACTION	98
4.8541-47.8257	0.1766	151	0.1469	2856	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	0.7991	-0.0533	-0.2783	1.7902	1.0058	1.6077	0.0101	-0.0813	0.0038	-0.0249	-0.0284	0.0066	-0.0402	0.0003	0.0227	0.0876	0.0038	-0.0078	0.1333	0.0187	0.1209	11.0374	104.1133	30.0678
2	1.1103	-0.3856	-0.776	3.564	-0.1001	1.477	0.0583	-0.1659	0.1237	0.2839	-0.092	-0.261	-0.083	0.0979	0.008	0.1523	-0.037	-0.0267	0.1885	-0.0301	0.1361	18.8502	111.7608	41.8135
3	0.9568	0.1909	0.0395	1.2094	0.154	1.0502	0.0076	0.0981	-0.0707	-0.1161	-0.0466	-0.0649	0.0483	0.0492	0.0274	0.1245	0.0072	0.0026	0.1222	-0.0044	0.1438	13.7248	91.6344	20.2432
4	2.1792	-0.5318	0.7095	0.3066	-0.4096	0.749	0.0405	-0.0083	-0.0586	-0.0172	-0.0008	-0.0097	0.0984	0.0091	-0.0508	0.1754	0.008	0.0039	0.1325	-0.012	0.1566	17.2833	118.7113	15.4723
5	2.6454	-0.2958	0.1774	2.1355	-1.6533	2.0465	0.0948	0.1688	-0.1215	-0.3278	-0.1803	-0.1095	0.3289	-0.1011	0.0761	0.1596	0.0285	0.0286	0.1829	-0.0192	0.173	36.4284	114.3443	18.5903
6	1.9555	-1.494	0.9007	5.2262	-3.1694	3.3232	0.0526	-0.1455	-0.0379	0.1585	-0.0476	-0.0758	-0.0337	0.1198	0.0238	0.1183	-0.0206	-0.0103	0.1866	-0.0208	0.1501	32.2272	113.9927	30.3129
7	1.8506	-0.5125	0.5729	3.2104	-1.3463	1.9852	0.0228	-0.0882	0.0413	0.1803	-0.1824	-0.2931	-0.0513	0.1406	0.1951	0.108	0.0084	-0.0202	0.2143	-0.0174	0.182	38.565	117.4844	27.1944
8	2.3806	-2.867	-0.7473	4.2087	-0.2495	1.811	-0.0016	-0.2181	0.3678	0.4097	0.0903	-0.4377	-0.381	0.06	-0.1351	0.1989	-0.0309	-0.0281	0.1789	-0.0341	0.2054	25.8485	127.2842	30.5314
9	1.6462	-0.1377	0.5007	1.0777	0.0497	1.8507	0.0308	0.1137	0.214	-0.0269	-0.0476	-0.0041	-0.0588	0.0631	0.019	0.1354	0.0169	0.0086	0.1262	0.0178	0.137	18.6205	125.3004	15.0811
10	2.4297	-1.126	-0.4169	2.8724	0.1948	3.4349	0.0047	0.0079	-0.0528	0.0651	0.0614	0.176	0.1024	-0.3349	-0.0422	0.1022	-0.0146	-0.0178	0.1111	0.0102	0.1244	1.619	123.819	9.6843
11	1.544	-2.5046	0.9433	4.8959	0.5807	5.1131	0.0207	0.1372	0.1301	-0.3746	-0.103	0.0585	-0.2128	-0.2512	0.03	0.1628	-0.02	-0.0215	0.2061	-0.0112	0.1949	0.4968	124.4966	2.886

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 225 through 323 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 324 through 399 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 400 through 530 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 225 through 292 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 293 through 323 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 324 through 352 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 353 through 380 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 381 through 399 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 400 through 464 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 465 through 513 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 514 through 530 )

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