PDB-4x0c: Crystal structure of P domain from norovirus strain NSW0514 in co...

ID or keywords:

Entry

Database: PDB / ID: 4x0c

Title

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

Components

VP1

Keywords

VIRAL PROTEIN / Viral capsid protein / 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: 1.72 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	Nov 21, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 4, 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 / diffrn_radiation_wavelength / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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	Jan 10, 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 / pdbx_initial_refinement_model / 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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Download

PDBx/mmCIF format	4x0c.cif.gz	366 KB	Display	PDBx/mmCIF format
PDB format	pdb4x0c.ent.gz	302.4 KB	Display	PDB format
PDBx/mmJSON format	4x0c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4x0c_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	4x0c_full_validation.pdf.gz	1.3 MB	Display
Data in XML	4x0c_validation.xml.gz	31 KB	Display
Data in CIF	4x0c_validation.cif.gz	48.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/4x0c ftp://data.pdbj.org/pub/pdb/validation_reports/x0/4x0c	HTTPS FTP

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Related structure data

Related structure data	4oosSC 4oovC 4ooxC 4op7C 4opoC 4opsC 4wzeC 4wzkC 4wzlC 4wztC 4x05C 4x06C 4x07C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4wzt-d 5iyr-d 2obs-1 4wze-d 3sld-2 5kon-d 3skb-3 3sld-3 3ony-2 4opo-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)

Deposited unit

A: VP1

B: VP1

hetero molecules

69.7 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)	104.830, 104.830, 191.000
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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 / End auth comp-ID: MET / End label comp-ID: MET

Dom-ID	Beg auth comp-ID	Beg label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	LYS	LYS	chain A	A	A	225 - 530	2 - 307
2	SER	SER	chain B	B	B	224 - 530	1 - 307

Details

biological unit is the same as asym.

#1: Protein

VP1

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

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

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4LM89

#2: Polysaccharide

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

Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis X antigen, alpha anomer

Descriptor	Type	Program
LFucpa1-3[DGalpb1-4]DGlcpNAca1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Chemical

ChemComp-FMT / FORMIC ACID

Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH₂O₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 747 / 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: 3.85 Å³/Da / Density % sol: 68.06 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium formate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: BM30A / Wavelength: 0.978196 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.978196 Å / Relative weight: 1

Reflection

Resolution: 1.7→45.95 Å / Num. obs: 116084 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / B_iso Wilson estimate: 20.39 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.068 / R_rim(I) all: 0.08 / Χ²: 0.934 / Net I/σ(I): 15.62 / Num. measured all: 421454

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.7-1.75		3.6	0.472	1.286	1.2	29113	8520	8319	1.513	97.6
1.75-1.79			0.634	1.047	1.6	30331	8314	8226	1.222	98.9
1.79-1.85			0.748	0.761	2.13	29756	8123	8063	0.889	99.3
1.85-1.9			0.805	0.617	2.57	28833	7863	7808	0.72	99.3
1.9-1.96			0.864	0.462	3.41	27788	7618	7562	0.54	99.3
1.96-2.03			0.913	0.334	4.6	27102	7412	7365	0.39	99.4
2.03-2.11			0.943	0.268	5.78	25458	7129	7039	0.314	98.7
2.11-2.2			0.966	0.196	7.54	25167	6891	6863	0.229	99.6
2.2-2.29			0.98	0.148	9.62	24151	6618	6587	0.173	99.5
2.29-2.41			0.988	0.113	12.17	23205	6329	6312	0.132	99.7
2.41-2.54			0.992	0.095	13.98	22138	6046	6034	0.111	99.8
2.54-2.69			0.995	0.073	17.57	20973	5740	5726	0.085	99.8
2.69-2.88			0.997	0.055	21.91	19629	5371	5363	0.065	99.9
2.88-3.11			0.998	0.041	27.61	18368	5049	5047	0.048	100
3.11-3.4			0.999	0.03	36.78	16817	4668	4655	0.035	99.7
3.4-3.8			0.999	0.024	46	14947	4223	4212	0.028	99.7
3.8-4.39			0.999	0.018	55.72	13057	3784	3759	0.022	99.3
4.39-5.38			1	0.015	63.12	11279	3225	3209	0.018	99.5
5.38-7.61			1	0.016	59.07	8927	2555	2546	0.019	99.6
	7.61		1	0.013	65.59	4415	1534	1389	0.016	90.5

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	4.67 Å	45.95 Å
Translation	4.67 Å	45.95 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.3	phasing
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4OOS

4oos

Resolution: 1.72→40.142 Å / FOM work R set: 0.8872 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1795	5621	5 %
R_work	0.1596	106840	-
obs	0.1606	112461	99.35 %

Solvent computation

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

Displacement parameters

B_iso max: 71.37 Å² / B_iso mean: 25.16 Å² / B_iso min: 10.59 Å²

Refinement step

Cycle: final / Resolution: 1.72→40.142 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4777	0	142	747	5666
B_iso mean	-	-	42.47	34.68	-
Num. residues	-	-	-	-	613

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	5086
X-RAY DIFFRACTION	f_angle_d	1.297	6938
X-RAY DIFFRACTION	f_chiral_restr	0.054	784
X-RAY DIFFRACTION	f_plane_restr	0.007	905
X-RAY DIFFRACTION	f_dihedral_angle_d	12.462	1874

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	2783	X-RAY DIFFRACTION	5.005	TORSIONAL
1	2	B	2783	X-RAY DIFFRACTION	5.005	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 (%)
1.72-1.7395	0.3208	184	0.2998	3494	X-RAY DIFFRACTION	99
1.7395-1.76	0.2935	183	0.2925	3487	X-RAY DIFFRACTION	99
1.76-1.7815	0.3024	184	0.277	3492	X-RAY DIFFRACTION	99
1.7815-1.804	0.285	186	0.2593	3532	X-RAY DIFFRACTION	99
1.804-1.8278	0.2564	184	0.2434	3485	X-RAY DIFFRACTION	99
1.8278-1.8528	0.212	184	0.2296	3524	X-RAY DIFFRACTION	99
1.8528-1.8793	0.2539	186	0.2206	3529	X-RAY DIFFRACTION	99
1.8793-1.9073	0.2508	185	0.2205	3513	X-RAY DIFFRACTION	99
1.9073-1.9371	0.254	185	0.2209	3513	X-RAY DIFFRACTION	99
1.9371-1.9689	0.2265	185	0.1985	3521	X-RAY DIFFRACTION	99
1.9689-2.0028	0.2098	186	0.199	3531	X-RAY DIFFRACTION	100
2.0028-2.0393	0.2103	184	0.1865	3501	X-RAY DIFFRACTION	99
2.0393-2.0785	0.22	184	0.2008	3490	X-RAY DIFFRACTION	98
2.0785-2.1209	0.1914	187	0.1683	3546	X-RAY DIFFRACTION	100
2.1209-2.167	0.1913	186	0.1648	3534	X-RAY DIFFRACTION	100
2.167-2.2174	0.17	187	0.1546	3563	X-RAY DIFFRACTION	100
2.2174-2.2729	0.1494	188	0.137	3559	X-RAY DIFFRACTION	100
2.2729-2.3343	0.159	187	0.1349	3553	X-RAY DIFFRACTION	100
2.3343-2.403	0.1652	187	0.1327	3550	X-RAY DIFFRACTION	100
2.403-2.4805	0.1606	188	0.1374	3573	X-RAY DIFFRACTION	100
2.4805-2.5692	0.1556	187	0.1373	3578	X-RAY DIFFRACTION	100
2.5692-2.672	0.1796	188	0.1399	3568	X-RAY DIFFRACTION	100
2.672-2.7936	0.1587	190	0.138	3611	X-RAY DIFFRACTION	100
2.7936-2.9409	0.1702	188	0.1468	3584	X-RAY DIFFRACTION	100
2.9409-3.125	0.1593	190	0.1537	3608	X-RAY DIFFRACTION	100
3.125-3.3662	0.1671	190	0.146	3625	X-RAY DIFFRACTION	100
3.3662-3.7048	0.1971	191	0.1561	3633	X-RAY DIFFRACTION	100
3.7048-4.2403	0.1477	192	0.1351	3665	X-RAY DIFFRACTION	100
4.2403-5.3404	0.1335	194	0.1181	3690	X-RAY DIFFRACTION	99
5.3404-40.14	0.1645	201	0.1595	3788	X-RAY DIFFRACTION	97

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	1.6442	0.0238	0.2639	1.8944	0.1129	1.2079	-0.0123	-0.1389	0.0014	-0.0099	0.0136	-0.0944	0.1011	0.0121	-0.0149	0.0969	0.0146	0.0089	0.1377	0.0072	0.1	-22.0945	23.0384	-24.4062
2	1.1557	0.6967	0.1599	2.5652	-0.4804	0.7014	-0.0556	-0.0774	0.3405	0.0303	-0.0115	0.3523	-0.1318	-0.3136	0.0181	0.1292	0.0744	-0.0035	0.2518	-0.0476	0.256	-33.7427	41.1308	-22.7905
3	0.9564	0.4121	0.3006	1.4855	0.388	1.3579	0.1017	-0.1681	-0.1845	0.18	-0.033	-0.1742	0.332	0.028	-0.0141	0.178	0.0315	-0.0188	0.1677	0.0425	0.1673	-20.6549	16.0914	-20.1734
4	0.9071	0.2336	0.5001	0.4892	0.3123	1.9893	-0.0203	-0.0026	0.018	-0.0048	-0.0084	-0.0453	-0.0475	0.0203	0.0307	0.1074	0.0297	-0.0132	0.1324	0.0125	0.1476	-8.623	36.882	-32.8165
5	2.4038	0.4804	-0.4817	0.2562	-0.1785	2.2845	0.0138	-0.2458	-0.0179	0.0997	-0.0796	-0.0519	-0.0892	0.0414	0.0625	0.1272	0.0156	-0.0273	0.1493	-0.0191	0.1304	-7.4645	40.484	-12.9479
6	1.5012	0.3568	-0.1166	1.0549	-0.5124	2.1801	0.0268	-0.2087	0.2355	0.1257	-0.0395	0.0385	-0.3361	0.0877	-0.0028	0.1701	0.0156	-0.033	0.143	-0.0382	0.1733	-6.9239	48.189	-18.1159
7	0.6892	-0.0798	-0.0089	1.0314	0.2783	1.6403	-0.0344	0.1522	0.0142	-0.1958	-0.0147	-0.004	-0.0707	0.0683	0.0489	0.1356	0.0219	-0.017	0.1745	0.0287	0.142	-9.9067	37.3232	-45.6678

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 225 through 292 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 293 through 380 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 381 through 530 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 224 through 292 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 293 through 352 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 353 through 418 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 419 through 530 )	B

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