PDB-4x1x: Crystal structure of RHDVb P domain in complex with Lewis Y

ID or keywords:

Entry

Database: PDB / ID: 4x1x

Title

Crystal structure of RHDVb P domain in complex with Lewis Y

Components

VP1

Keywords

VIRAL PROTEIN / Major Capsid Protein / Capsid spike / Protruding domain / HBGA binding

Function / homology

Calicivirus coat protein / Calicivirus coat protein / H type 2 antigen, alpha anomer / VP1

Function and homology information

Biological species

Rabbit hemorrhagic disease virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Leuthold, M.M. / Hansman, G.S.

Citation

Journal: J.Virol. / Year: 2015
Title: Structural analysis of a rabbit hemorrhagic disease virus binding to histo-blood group antigens.
Authors: Leuthold, M.M. / Dalton, K.P. / Hansman, G.S.

History

Deposition	Nov 25, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jan 14, 2015	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 / 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_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 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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PDBx/mmCIF format	4x1x.cif.gz	364 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4x1x_validation.pdf.gz	789 KB	Display	wwPDB validaton report
Full document	4x1x_full_validation.pdf.gz	790.4 KB	Display
Data in XML	4x1x_validation.xml.gz	30.3 KB	Display
Data in CIF	4x1x_validation.cif.gz	47.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x1/4x1x ftp://data.pdbj.org/pub/pdb/validation_reports/x1/4x1x	HTTPS FTP

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Related structure data

Related structure data	4x1wSC 4x1zC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4x1w-2 4x1z-d 4egt-d 4x1w-1 2q66-d 2g04-1 1o96-1 4i2s-d 1o96-3 2i9d-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 (2)

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)	59.440, 84.150, 62.660
Angle α, β, γ (deg.)	90.000, 110.110, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	chain A	A	A	238 - 569	3 - 334
2	chain B	B	B	236 - 569	1 - 334

Details

The biological unit is a dimer. There is 1 biological unit in the asymmetric unit (chains A & B)

#1: Protein

VP1

Mass: 34430.020 Da / Num. of mol.: 2 / Fragment: UNP residues 236-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rabbit hemorrhagic disease virus / Gene: VP1 / Production host:

Escherichia coli (E. coli) / References: UniProt: I7FLU3

#2: Polysaccharide

alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / H type 2 antigen / alpha anomer

Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: H type 2 antigen, alpha anomer

Descriptor	Type	Program
LFucpa1-2DGalpb1-4DGlcpNAca1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}	LINUCS	PDB-CARE

#3: Chemical

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

Mass: 62.068 Da / Num. of mol.: 3 / Fragment: ligand / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Chemical

ChemComp-CL / CHLORIDE ION

Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 662 / 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: 2.14 Å³/Da / Density % sol: 42.44 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: Lithium chloride, PEG 6000, Citric Acid

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.984463 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2013

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.984463 Å / Relative weight: 1

Reflection

Resolution: 1.55→48.22 Å / Num. obs: 153487 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 3 % / B_iso Wilson estimate: 14.29 Å² / R_merge F obs: 0.996 / R_merge(I) obs: 0.061 / R_rim(I) all: 0.085 / Χ²: 0.921 / Net I/σ(I): 7.46 / Num. measured all: 243456

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	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
1.55-1.59		0.564	0.484	1.34	17153	12299	10733	0.671	87.3
1.59-1.63		0.658	0.391	1.65	17660	11918	11043	0.542	92.7
1.63-1.68		0.743	0.328	1.92	16152	11562	10401	0.454	90
1.68-1.73		0.823	0.26	2.44	16962	11294	10628	0.361	94.1
1.73-1.79		0.867	0.216	3.05	16876	10938	10356	0.3	94.7
1.79-1.85		0.911	0.179	3.65	15995	10516	9929	0.249	94.4
1.85-1.92		0.935	0.144	4.53	15172	10213	9552	0.2	93.5
1.92-2		0.952	0.124	5.4	13737	9793	8951	0.172	91.4
2-2.09		0.97	0.097	6.68	13994	9397	8878	0.136	94.5
2.09-2.19		0.975	0.086	7.85	13785	9027	8580	0.12	95
2.19-2.31		0.982	0.072	9.12	12962	8533	8114	0.101	95.1
2.31-2.45		0.986	0.062	10.33	11908	8059	7547	0.086	93.6
2.45-2.62		0.988	0.055	11.31	10336	7595	6865	0.077	90.4
2.62-2.83		0.992	0.047	13.32	10982	7111	6766	0.066	95.1
2.83-3.1		0.993	0.04	15.19	9782	6491	6096	0.056	93.9
3.1-3.47		0.994	0.036	17.22	8640	5902	5486	0.051	93
3.47-4		0.996	0.03	18.45	6941	5164	4635	0.042	89.8
4-4.9		0.996	0.027	21.21	6686	4394	4092	0.038	93.1
4.9-6.94		0.997	0.025	20.39	4928	3387	3091	0.035	91.3
	6.94	0.996	0.026	22.18	2805	1854	1744	0.037	94.1

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4x1w

4x1w

Resolution: 1.6→48.22 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 17.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1845	7012	4.99 %
R_work	0.1545	133427	-
obs	0.1561	140439	93.31 %

Solvent computation

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

Displacement parameters

B_iso max: 75.88 Å² / B_iso mean: 18.7441 Å² / B_iso min: 7.31 Å²

Refinement step

Cycle: final / Resolution: 1.6→48.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4846	0	51	663	5560
B_iso mean	-	-	23.74	26.66	-
Num. residues	-	-	-	-	666

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5060
X-RAY DIFFRACTION	f_angle_d	1.081	6954
X-RAY DIFFRACTION	f_chiral_restr	0.042	788
X-RAY DIFFRACTION	f_plane_restr	0.005	919
X-RAY DIFFRACTION	f_dihedral_angle_d	10.92	1750

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	3576	X-RAY DIFFRACTION	6.021	TORSIONAL
1	2	B	3576	X-RAY DIFFRACTION	6.021	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.6182	0.2961	221	0.2447	4422	4643	93
1.6182-1.6372	0.3154	235	0.2428	4446	4681	93
1.6372-1.6572	0.2782	232	0.2402	4389	4621	92
1.6572-1.6782	0.2829	224	0.2344	4157	4381	89
1.6782-1.7003	0.2565	231	0.2229	4414	4645	92
1.7003-1.7235	0.2213	235	0.2082	4474	4709	95
1.7235-1.7482	0.2285	240	0.199	4613	4853	95
1.7482-1.7743	0.2285	238	0.2041	4438	4676	94
1.7743-1.802	0.2522	237	0.1906	4520	4757	95
1.802-1.8315	0.2205	236	0.1847	4476	4712	95
1.8315-1.8631	0.2121	231	0.1741	4549	4780	95
1.8631-1.897	0.2059	235	0.1686	4493	4728	94
1.897-1.9335	0.1641	231	0.1584	4401	4632	93
1.9335-1.973	0.1748	233	0.1539	4452	4685	93
1.973-2.0159	0.1958	226	0.1637	4262	4488	89
2.0159-2.0627	0.1922	241	0.158	4554	4795	95
2.0627-2.1143	0.1966	237	0.1556	4496	4733	95
2.1143-2.1715	0.1973	238	0.1526	4520	4758	95
2.1715-2.2354	0.1647	247	0.1403	4575	4822	95
2.2354-2.3075	0.159	235	0.1377	4489	4724	95
2.3075-2.39	0.1739	243	0.1383	4526	4769	94
2.39-2.4857	0.1743	226	0.1426	4405	4631	93
2.4857-2.5988	0.1702	228	0.143	4304	4532	89
2.5988-2.7358	0.1584	243	0.144	4484	4727	95
2.7358-2.9072	0.1762	235	0.1443	4534	4769	95
2.9072-3.1317	0.1833	233	0.142	4476	4709	94
3.1317-3.4467	0.1828	230	0.1454	4427	4657	93
3.4467-3.9453	0.1581	228	0.1436	4281	4509	90
3.9453-4.9698	0.1552	233	0.1223	4445	4678	93
4.9698-48.2427	0.1571	230	0.1409	4405	4635	92

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	1.2623	-1.6137	-0.3246	5.8276	4.4594	5.0611	-0.1192	-0.075	-0.036	0.4284	0.1439	-0.0357	0.1889	-0.0502	-0.0336	0.1157	0.0081	0.0003	0.0934	0.0254	0.11	-36.4833	27.1939	-33.1228
2	1.0619	-0.2027	-0.2266	2.1741	0.522	0.4728	-0.05	0.0453	-0.1575	-0.0158	0.0602	0.3981	0.0612	-0.1034	-0.0095	0.0816	0.0035	-0.0104	0.12	0.0046	0.1689	-43.0261	18.1286	-38.5683
3	4.26	-1.4108	-3.1233	1.8987	1.5288	3.9975	-0.1583	-0.0531	-0.2657	0.0244	-0.0398	0.372	0.226	-0.0686	0.2146	0.1223	-0.0122	-0.0409	0.0932	0.0049	0.2179	-36.0463	-0.8195	-47.4016
4	2.5412	1.4817	1.3833	5.455	-1.6511	2.9519	0.0619	0.4152	-0.3356	-0.4648	-0.0148	-0.0661	0.158	0.274	-0.0504	0.0957	0.0306	-0.0517	0.1582	-0.055	0.1782	-34.4542	11.8916	-53.8896
5	0.7067	-0.5999	0.0434	0.9521	0.0021	0.6025	0.036	0.0265	-0.1372	-0.1265	-0.0547	0.2517	0.0873	-0.1112	0.0055	0.1071	-0.0159	-0.0311	0.1005	-0.0175	0.1449	-32.1474	5.2088	-49.8187
6	0.8727	-0.3057	-0.5409	1.0068	0.2745	1.0069	0.0314	0.0436	-0.0212	-0.1484	-0.063	0.2331	-0.0981	-0.1117	0.0166	0.1105	0.0093	-0.0406	0.1005	0.0025	0.1619	-39.8295	23.9952	-46.8212
7	1.9146	-1.059	-0.0099	1.1716	0.4344	1.3261	0.0986	-0.1231	0.1145	0.066	0.1102	0.3282	-0.187	-0.3136	-0.1716	0.0938	0.0088	0.0033	0.1227	-0.0016	0.2094	-41.2954	25.413	-35.558
8	1.5205	-0.2974	1.0215	1.7002	0.671	2.6288	-0.0103	-0.0147	0.1091	-0.0379	0.0261	0.2914	-0.2697	-0.079	-0.0236	0.1269	0.0313	0.0023	0.1107	0.007	0.1811	-44.8712	37.6912	-36.4818
9	1.5767	0.1276	-0.8049	0.5862	-0.1336	2.0578	-0.0012	0.0435	0.0209	0.0577	-0.0158	0.0236	-0.0761	-0.1216	0.0255	0.0883	0.0041	0.004	0.0794	-0.0039	0.0808	-23.3418	18.8495	-22.5556
10	4.9208	0.1322	-0.015	3.2066	1.7548	5.6184	-0.0183	0.1597	0.0278	-0.3921	0.0444	-0.2313	0.0704	0.1476	0.0085	0.1322	0.008	0.0344	0.1249	0.0306	0.0685	-6.837	6.8453	-49.7145
11	0.4341	0.024	-0.1892	0.7392	0.015	1.3513	0.0013	0.034	0.0157	-0.0138	0.0133	-0.0273	0.0084	0.0492	-0.0135	0.0848	0.0016	0.0157	0.1012	0.0053	0.1069	-11.3556	10.6203	-38.7043
12	0.8607	-0.052	0.5997	1.3375	1.9501	3.4961	-0.0136	-0.1145	-0.0288	0.1391	-0.0464	0.0604	0.2337	-0.0947	0.07	0.1042	0.0031	0.0254	0.0836	0.0307	0.0908	-18.4059	8.9965	-20.8882
13	1.0308	-0.4066	-0.4402	0.6264	0.2289	1.5207	-0.1131	-0.0585	-0.1175	0.0607	-0.0199	0.1029	0.1187	-0.1073	0.1026	0.1079	-0.0137	0.0177	0.1053	-0.0035	0.0968	-26.8403	15.8044	-13.5147
14	4.5709	1.6117	0.7957	3.1787	-1.7264	4.4436	-0.0086	-0.3453	0.0499	0.2698	-0.1559	-0.0235	-0.0343	-0.0997	0.1882	0.1619	0.0298	0.0444	0.1553	-0.0389	0.0823	-29.2559	17.4053	-3.2979

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 238 through 260 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 261 through 297 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 298 through 334 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 335 through 354 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 355 through 436 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 437 through 476 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 477 through 510 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 511 through 569 )	A
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 236 through 297 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 298 through 314 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 315 through 436 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 437 through 476 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 477 through 551 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 552 through 569 )	B

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