PDB-4op7: Crystal structure of P domain from norovirus strain NSW0514 in co...

ID or keywords:

Entry

Database: PDB / ID: 4op7

Title

Crystal structure of P domain from norovirus strain NSW0514 in complex with HBGA type B (triglycan)

Components

VP1

Keywords

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

Function / homology

Function and homology information

virion component / host cell cytoplasm
Similarity search - Function

Biological species

Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.92 Å

Authors

Singh, B.K. / 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 5, 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details 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	4op7.cif.gz	354.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4op7_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	4op7_full_validation.pdf.gz	1.2 MB	Display
Data in XML	4op7_validation.xml.gz	27.4 KB	Display
Data in CIF	4op7_validation.cif.gz	41 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/op/4op7 ftp://data.pdbj.org/pub/pdb/validation_reports/op/4op7	HTTPS FTP

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Related structure data

Related structure data	4oosC 4oovC 4ooxC 4opoC 4opsC 4wzeC 4wzkC 4wzlC 4wztC 4x05C 4x06C 4x07C 4x0cC C: citing same article (ref.)
Similar structure data	5j35-d 4x0c-d 5iyr-d 4wze-d 3sej-1 5lfe-d 4x05-2 6b58-1 4opo-d 4wzk-d Search similar-shape structures by Omokage search (details) 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	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (4) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: VP1

B: VP1

hetero molecules

69.2 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)	104.610, 104.610, 190.540
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

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: 2 - 307

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

#1: Protein

VP1

Mass: 34060.961 Da / Num. of mol.: 2 / Fragment: P domain NSW0514 (UNP residues 225-530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Gene: JX459908 / Plasmid: MBP-HTSHP / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K4LM89

#2: Polysaccharide

alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose

Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
LFucpa1-2[DGalpa1-3]DGalpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2112h-1a_1-5][a1221m-1a_1-5]/1-2-1/a2-b1_a3-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-IMD / IMIDAZOLE

Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₅N₂

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 492 / 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: 3.83 Å³/Da / Density % sol: 67.85 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: PEG 3350, Sodium 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: BM30A / Wavelength: 0.978174 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2013

Radiation

Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.978174 Å / Relative weight: 1

Reflection

Resolution: 1.9→48.19 Å / Num. obs: 78721 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / B_iso Wilson estimate: 22.39 Å² / R_merge(I) obs: 0.113 / Net I/σ(I): 10.7

Reflection shell

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.9-1.95		3.6	0.012	1.09	1	93.7
1.95-2			0.012	1.35	1	96.8
2-2.06			0.012	1.97	1	95.8
2.06-2.12			0.012	2.17	1	96
2.12-2.19			0.012	2.79	1	96.2
2.19-2.27			0.012	3.45	1	96.1
2.27-2.36			0.012	4.1	1	95.8
2.36-2.45			0.012	4.76	1	95.5
2.45-2.56			0.012	5.69	1	94.8
2.56-2.69			0.012	6.95	1	94.2
2.69-2.83			0.012	9.01	1	93.9
2.83-3			0.012	11.38	1	93.1
3-3.21			0.012	16.96	1	92.3
3.21-3.47			0.012	22.58	1	91.6
3.47-3.8			0.012	28.13	1	90.6
3.8-4.25			0.012	34.74	1	90.2
4.25-4.91			0.012	41.32	1	89.7
4.91-6.01			0.012	37.61	1	88.8
6.01-8.5			0.012	38.25	1	87.1
	8.5		0.012	45.1	1	77.9

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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: 1.92→48.187 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 21.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2081	3817	5 %
R_work	0.1847	-	-
obs	0.1859	76345	93.92 %

Solvent computation

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

Displacement parameters

B_iso mean: 27.51 Å²

Refinement step

Cycle: LAST / Resolution: 1.92→48.187 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4762	0	76	492	5330

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4983
X-RAY DIFFRACTION	f_angle_d	1.102	6814
X-RAY DIFFRACTION	f_dihedral_angle_d	13.584	1850
X-RAY DIFFRACTION	f_chiral_restr	0.044	750
X-RAY DIFFRACTION	f_plane_restr	0.007	893

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 (%)
1.92-1.9443	0.344	143	0.3312	2725	X-RAY DIFFRACTION	96
1.9443-1.9699	0.2903	143	0.3029	2723	X-RAY DIFFRACTION	97
1.9699-1.9969	0.3061	144	0.2957	2722	X-RAY DIFFRACTION	96
1.9969-2.0254	0.299	143	0.2931	2722	X-RAY DIFFRACTION	97
2.0254-2.0557	0.3076	141	0.3088	2674	X-RAY DIFFRACTION	95
2.0557-2.0878	0.3255	142	0.295	2693	X-RAY DIFFRACTION	95
2.0878-2.122	0.2946	142	0.2488	2701	X-RAY DIFFRACTION	96
2.122-2.1586	0.2905	144	0.2403	2722	X-RAY DIFFRACTION	96
2.1586-2.1979	0.2573	142	0.2316	2711	X-RAY DIFFRACTION	96
2.1979-2.2401	0.2283	144	0.2084	2723	X-RAY DIFFRACTION	96
2.2401-2.2859	0.2589	143	0.2142	2726	X-RAY DIFFRACTION	96
2.2859-2.3356	0.2164	143	0.207	2714	X-RAY DIFFRACTION	96
2.3356-2.3899	0.274	143	0.2035	2701	X-RAY DIFFRACTION	95
2.3899-2.4496	0.235	142	0.2044	2707	X-RAY DIFFRACTION	96
2.4496-2.5159	0.2356	143	0.1935	2706	X-RAY DIFFRACTION	95
2.5159-2.5899	0.211	141	0.1846	2681	X-RAY DIFFRACTION	95
2.5899-2.6735	0.2287	142	0.1792	2691	X-RAY DIFFRACTION	94
2.6735-2.769	0.2138	141	0.1694	2679	X-RAY DIFFRACTION	94
2.769-2.8799	0.2235	140	0.1665	2650	X-RAY DIFFRACTION	93
2.8799-3.0109	0.195	141	0.166	2680	X-RAY DIFFRACTION	93
3.0109-3.1697	0.1763	140	0.1528	2665	X-RAY DIFFRACTION	93
3.1697-3.3682	0.1624	138	0.1548	2635	X-RAY DIFFRACTION	91
3.3682-3.6282	0.1955	139	0.1551	2634	X-RAY DIFFRACTION	91
3.6282-3.9931	0.1587	137	0.1459	2628	X-RAY DIFFRACTION	91
3.9931-4.5706	0.1405	138	0.1253	2630	X-RAY DIFFRACTION	90
4.5706-5.7569	0.1361	140	0.1356	2641	X-RAY DIFFRACTION	89
5.7569-48.2026	0.2003	138	0.1815	2644	X-RAY DIFFRACTION	84

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	1.0382	-0.1054	-0.1726	0.5707	0.4691	2.7825	-0.0514	-0.0403	-0.0365	-0.0401	0.0578	-0.0268	0.0476	0.0204	-0.004	0.0997	-0.0004	0.0186	0.136	0.0227	0.1334	43.9611	15.4986	-14.966
2	2.0907	-0.6798	0.4114	0.3903	-0.2833	2.2337	0.0528	0.2329	-0.1636	-0.1866	-0.0367	0.0245	0.0764	0.0487	0.0141	0.1901	-0.0012	0.0308	0.1308	-0.0297	0.156	43.7533	8.5902	-34.2959
3	0.6753	-0.0595	0.2253	1.1748	0.5486	1.8973	-0.0152	-0.2114	-0.0666	0.1926	0.0016	-0.018	0.0294	0.0477	0.0145	0.1332	-0.0022	0.0093	0.2041	0.0577	0.1445	44.2956	13.1902	-5.2943
4	2.1845	-0.0238	-0.335	2.6366	0.4848	1.2997	-0.0539	0.0143	0.1765	0.2279	0.1946	-0.4744	-0.1884	-0.0214	-0.1207	0.1931	0.0442	-0.045	0.1645	-0.0295	0.1993	30.3683	29.2717	-23.096
5	2.0691	-0.492	-0.3459	3.6377	-0.8144	1.3083	0.0015	0.123	-0.2641	-0.1655	-0.0463	0.324	0.0074	-0.2857	0.0084	0.1253	-0.0091	-0.0313	0.2266	-0.0342	0.1976	19.7919	12.4668	-27.2126
6	0.6873	-1.0504	-0.4268	2.3024	0.6466	1.4104	0.1161	0.0489	0.4383	-0.0377	0.1931	-0.7396	-0.324	0.2114	-0.2155	0.2398	-0.0013	0.0136	0.2032	-0.0532	0.4142	32.9452	38.6261	-25.7867

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 224 through 292 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 293 through 398 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 399 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 398 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 399 through 530 )

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