PDB-4drr: Cell attachment protein VP8* of a human rotavirus specifically in...

ID or keywords:

Entry

Database: PDB / ID: 4drr

Title

Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen

Components

Outer capsid protein VP4

Keywords

VIRAL PROTEIN / OTAVIRUS / CELL ATTACHMENT FACTOR / HISTO BLOOD GROUP ANTIGEN / GALECTIN-FOLD

Function / homology

Function and homology information

host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane /

membrane
Similarity search - Function

Biological species

Rotavirus sp.

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Hu, L. / Crawford, S.E. / Czako, R. / Cortes-Penfield, N.W. / Smith, D.F. / Le Pendu, J. / Estes, M.K. / Prasad, B.V.V.

Citation

Journal: Nature / Year: 2012
Title: Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen.
Authors: Hu, L. / Crawford, S.E. / Czako, R. / Cortes-Penfield, N.W. / Smith, D.F. / Le Pendu, J. / Estes, M.K. / Prasad, B.V.

History

Deposition	Feb 17, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 11, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 23, 2012	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4drr.cif.gz	86.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4drr.ent.gz	64.4 KB	Display	PDB format
PDBx/mmJSON format	4drr.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/dr/4drr ftp://data.pdbj.org/pub/pdb/validation_reports/dr/4drr	HTTPS FTP

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Related structure data

Related structure data	4drvC 4ds0C 1kqrS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ymt-12 5vx4-d 3sit-1 5ymt-6 5yms-8 2p3k-d 5ymt-8 2p3i-d 6h9z-1 6ha0-2 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

Deposited unit

A: Outer capsid protein VP4

hetero molecules

18.6 kDa, 1 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)	43.758, 34.923, 44.096
Angle α, β, γ (deg.)	90.00, 95.46, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Outer capsid protein VP4 / Rotavirus cell attachment protein VP8* Mass: 18567.623 Da / Num. of mol.: 1 / Fragment: UNP residues 64-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus sp. / Gene: VP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86169
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 319 / 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: 1.81 Å³/Da / Density % sol: 31.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 30% PEG 1500 Sodium acetate trihydrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 7, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.5→23.8 Å / Num. all: 20539 / Num. obs: 20539 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 1.5→1.55 Å / % possible all: 75.4

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Processing

Software

Name: PHENIX / Version: (phenix.refine: dev_516) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1KQR

1kqr

Resolution: 1.5→23.793 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 20.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.216	1048	5.1 %	Random
R_work	0.1785	-	-	-
all	0.1804	20536	-	-
obs	0.1804	20536	95.61 %	-

Solvent computation

Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 20 Å² / k_sol: 0.4 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.857 Å²	0 Å²	1.1259 Å²
2-	-	1.6629 Å²	0 Å²
3-	-	-	0.8976 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→23.793 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1307	0	1	319	1627

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1339
X-RAY DIFFRACTION	f_angle_d	1.057	1830
X-RAY DIFFRACTION	f_dihedral_angle_d	12.127	477
X-RAY DIFFRACTION	f_chiral_restr	0.067	203
X-RAY DIFFRACTION	f_plane_restr	0.004	235

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 (%)
1.5-1.5791	0.7719	120	0.6282	2315	X-RAY DIFFRACTION	80
1.5791-1.678	0.3851	160	0.3565	2752	X-RAY DIFFRACTION	96
1.678-1.8075	0.2769	155	0.2137	2808	X-RAY DIFFRACTION	97
1.8075-1.9894	0.2103	145	0.1648	2843	X-RAY DIFFRACTION	98
1.9894-2.277	0.2068	145	0.1591	2876	X-RAY DIFFRACTION	99
2.277-2.868	0.2118	157	0.1533	2914	X-RAY DIFFRACTION	100
2.868-23.7958	0.1427	166	0.1319	2980	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	0.2185	0.005	0.268	1.1664	0.449	0.8177	-0.0807	0.0847	0.019	0.0182	-0.1472	-0.251	0.056	0.2925	0.1845	0.0763	0.0006	0.0216	0.1309	0.0309	0.0663	28.7687	15.0566	16.8915
2	0.1495	0.1472	-0.0337	0.3008	0.0933	0.0688	-0.0208	0.0369	-0.0069	-0.0962	-0.0225	0.0622	-0.0027	-0.009	0.0351	0.081	0.0018	-0.0006	0.0587	0.0017	0.0677	23.7651	10.5278	27.8821
3	1.5391	-0.3379	-0.4188	0.2247	-0.1997	2.2318	-0.3158	-0.1707	0.0717	0.066	0.1426	0.1848	0.0617	-0.2873	0.0886	0.0603	0.0108	-0.0184	0.015	-0.0024	0.0314	37.1665	15.1698	35.2525
4	0.9001	0.2712	0.0183	1.0472	0.0444	0.5809	-0.054	0.2575	0.1038	0.1976	0.1695	-0.0465	0.0082	-0.2037	-0.0447	0.0651	-0.0226	0.0044	0.0796	0.0088	0.0491	22.6118	5.134	41.0488
5	0.7094	0.5867	-0.2478	0.8077	-0.5501	0.5457	-0.0089	0.0545	0.1602	-0.1261	0.0345	-0.002	0.0914	0.0728	-0.0584	0.0865	-0.0168	0.005	0.0657	-0.0165	0.0717	26.2636	2.3292	41.1278
6	0.4213	-0.1072	-0.1007	0.3002	0.0169	0.4464	-0.0057	0.0856	0.0002	0.0681	-0.0779	0.0202	0.033	-0.0711	0.0208	0.054	0.0033	0.0116	0.0609	-0.0046	0.0436	46.1179	9.2778	36.1572
7	1.6642	-0.9214	-0.1363	0.8976	0.2231	0.5249	-0.1523	-0.0456	0.1078	0.3163	-0.0521	-0.0942	0.0094	0.0278	0.1401	0.0699	-0.0156	0.0079	0.0826	0.007	0.0746	46.2805	7.8585	45.8558
8	0.171	0.1716	0.0063	0.3936	-0.0042	0.2952	-0.0049	-0.0839	0.0382	0.1046	-0.0003	-0.0499	-0.1389	0.0476	-0.071	0.0689	-0.0072	0.0071	0.072	-0.0136	0.0923	33.9567	9.9467	47.7321
9	0.5825	-0.1135	-0.6747	0.2425	0.1674	0.9306	-0.1184	-0.1386	0.0106	0.0841	0.1063	0.1465	0.2907	-0.008	0.0191	0.0764	0.0102	0.0178	0.0988	0.0018	0.0526	47.6698	3.4901	38.6904
10	1.2084	0.2279	0.2576	0.1218	0.1579	0.5572	0.1523	0.1791	0.0469	0.1005	0.0112	0.0794	-0.221	0.1567	-0.1235	0.0731	0.0086	0.0327	0.121	-0.0088	0.0656	47.5182	7.3832	30.2909
11	1.7192	-0.0477	-1.0939	0.1716	0.0851	1.171	-0.0609	-0.2438	0.1312	0.0898	0.0291	0.112	0.1364	0.0077	-0.0011	0.0523	-0.0133	0.0116	0.0733	-0.0014	0.0433	32.2576	1.879	41.4495
12	1.2205	-0.614	-0.0359	0.7309	0.0496	0.4675	-0.0639	0.1031	0.2407	-0.0547	0.0026	-0.1156	-0.0462	-0.0053	0.007	0.0185	0.0015	0.0177	0.0544	-0.0077	0.022	31.2284	0.7572	46.1833
13	0.1343	0.1392	0.0272	0.308	-0.2547	0.4787	0.0691	-0.0456	0.2287	-0.0575	0.0177	0.1212	0.0669	-0.1205	-0.0061	0.0742	-0.0073	0.0077	0.0885	0.0244	0.0385	41.1915	2.8983	29.6288
14	1.262	0.569	-0.2466	0.6158	-0.3042	0.4836	-0.0941	-0.0387	0.0291	-0.1206	-0.0156	-0.0433	0.0454	0.1346	0.0477	0.0696	-0.0118	0.0009	0.0762	0.0053	0.0651	30.5076	5.1304	27.5774
15	1.1272	0.0566	-0.0167	-0.0144	0.0112	0.011	0.1941	-0.062	0.2209	0.0501	-0.1139	0.0416	0.0659	0.0247	-0.0224	0.0476	-0.012	0.0056	0.0673	0.0019	0.0507	29.7339	-2.1054	28.9976
16	0.2775	-0.0332	-0.0915	0.071	-0.0844	0.4894	0.0712	-0.0353	-0.1167	-0.0426	-0.0576	-0.0245	-0.0495	0.0847	-0.0034	0.0641	0.011	0.016	0.0461	-0.0121	0.0616	32.5187	-3.2012	28.6797
17	0.0845	0.1318	0.0619	0.4837	-0.1167	0.2096	-0.0114	0.0944	-0.0186	-0.083	0.0376	0.1393	-0.0352	-0.0358	0.0182	0.0521	0.0114	0.0083	0.0593	-0.0035	0.068	21.3345	7.3944	35.2195
18	0.4975	0.5273	0.1388	0.7087	0.2302	0.5235	-0.0205	-0.1059	0.0569	0.0385	-0.0342	0.1112	-0.0745	-0.1211	-0.0234	0.0717	-0.0102	-0.0029	0.0464	-0.0022	0.0379	26.4131	10.1298	22.8534
19	0.2	0.0205	0.4741	0.7072	0.2039	1.4092	-0.0187	0.0574	0.0019	-0.0079	-0.0692	0.0661	-0.151	0.1265	0.0912	0.0988	0.0107	0.0111	0.09	-0.0077	0.0757	28.6128	3.115	16.1284
20	0.4784	-0.059	-0.0425	0.5306	-0.1352	0.0847	0.0263	0.0046	0.0337	-0.4205	0.0213	0.0774	0.2441	0.0857	0.0293	0.0791	0.0156	-0.0068	0.0685	-0.0017	0.0802	36.7481	6.3616	18.2825

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 62:68)
2	X-RAY DIFFRACTION	2	(chain A and resid 69:85)
3	X-RAY DIFFRACTION	3	(chain A and resid 86:92)
4	X-RAY DIFFRACTION	4	(chain A and resid 93:99)
5	X-RAY DIFFRACTION	5	(chain A and resid 100:105)
6	X-RAY DIFFRACTION	6	(chain A and resid 106:112)
7	X-RAY DIFFRACTION	7	(chain A and resid 113:118)
8	X-RAY DIFFRACTION	8	(chain A and resid 119:128)
9	X-RAY DIFFRACTION	9	(chain A and resid 129:134)
10	X-RAY DIFFRACTION	10	(chain A and resid 135:139)
11	X-RAY DIFFRACTION	11	(chain A and resid 140:147)
12	X-RAY DIFFRACTION	12	(chain A and resid 148:155)
13	X-RAY DIFFRACTION	13	(chain A and resid 156:161)
14	X-RAY DIFFRACTION	14	(chain A and resid 162:170)
15	X-RAY DIFFRACTION	15	(chain A and resid 171:180)
16	X-RAY DIFFRACTION	16	(chain A and resid 181:192)
17	X-RAY DIFFRACTION	17	(chain A and resid 193:203)
18	X-RAY DIFFRACTION	18	(chain A and resid 204:210)
19	X-RAY DIFFRACTION	19	(chain A and resid 211:216)
20	X-RAY DIFFRACTION	20	(chain A and resid 217:224)

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