PDB-4pch: Structure of Human Polyomavirus 7 (HPyV7) VP1 pentamer

ID or keywords:

Entry

Database: PDB / ID: 4pch

Title

Structure of Human Polyomavirus 7 (HPyV7) VP1 pentamer

Components

VP1

Keywords

VIRAL PROTEIN / major viral capsid protein / jelly-roll topology / attachment to host-cell receptors

Function / homology

Function and homology information

viral process /

viral capsid / host cell nucleus / structural molecule activity /

nucleus
Similarity search - Function

Biological species

Polyomavirus HPyV7

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Stroh, L.J. / Stehle, T.

Citation

Journal: J.Virol. / Year: 2014
Title: Structure analysis of the major capsid proteins of human polyomaviruses 6 and 7 reveals an obstructed sialic Acid binding site.
Authors: Stroh, L.J. / Neu, U. / Blaum, B.S. / Buch, M.H. / Garcea, R.L. / Stehle, T.

History

Deposition	Apr 15, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 6, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 3, 2014	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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	4pch.cif.gz	512.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4pch.ent.gz	424.1 KB	Display	PDB format
PDBx/mmJSON format	4pch.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/pc/4pch ftp://data.pdbj.org/pub/pdb/validation_reports/pc/4pch	HTTPS FTP

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Related structure data

Related structure data	4pcgC 3s7xS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4pcg-d 3nxd-d 4x16-d 3nxg-d 4x15-d 4jce-d 6hkv-1 4x13-d 4x0y-d 6y61-2 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
Related items in Molecule of the Month	#47 - Nov 2003 Simian Virus 40 similarity (4) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (4)

Deposited unit

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

hetero molecules

147 kDa, 5 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)	209.670, 86.430, 84.210
Angle α, β, γ (deg.)	90.00, 92.14, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	VAL	GLY	GLY	A	A	28 - 47	13 - 32
2	1	VAL	VAL	GLY	GLY	B	B	28 - 47	13 - 32
3	1	VAL	VAL	GLY	GLY	C	C	28 - 47	13 - 32
4	1	VAL	VAL	GLY	GLY	D	D	28 - 47	13 - 32
5	1	VAL	VAL	GLY	GLY	E	E	28 - 47	13 - 32
1	2	GLN	GLN	VAL	VAL	A	A	56 - 80	41 - 65
2	2	GLN	GLN	VAL	VAL	B	B	56 - 80	41 - 65
3	2	GLN	GLN	VAL	VAL	C	C	56 - 80	41 - 65
4	2	GLN	GLN	VAL	VAL	D	D	56 - 80	41 - 65
5	2	GLN	GLN	VAL	VAL	E	E	56 - 80	41 - 65
1	3	TRP	TRP	LEU	LEU	A	A	98 - 155	83 - 140
2	3	TRP	TRP	LEU	LEU	B	B	98 - 155	83 - 140
3	3	TRP	TRP	LEU	LEU	C	C	98 - 155	83 - 140
4	3	TRP	TRP	LEU	LEU	D	D	98 - 155	83 - 140
5	3	TRP	TRP	LEU	LEU	E	E	98 - 155	83 - 140
1	4	VAL	VAL	THR	THR	A	A	169 - 251	154 - 236
2	4	VAL	VAL	THR	THR	B	B	169 - 251	154 - 236
3	4	VAL	VAL	THR	THR	C	C	169 - 251	154 - 236
4	4	VAL	VAL	THR	THR	D	D	169 - 251	154 - 236
5	4	VAL	VAL	THR	THR	E	E	169 - 251	154 - 236
1	5	VAL	VAL	ARG	ARG	A	A	269 - 278	254 - 263
2	5	VAL	VAL	ARG	ARG	B	B	269 - 278	254 - 263
3	5	VAL	VAL	ARG	ARG	C	C	269 - 278	254 - 263
4	5	VAL	VAL	ARG	ARG	D	D	269 - 278	254 - 263
5	5	VAL	VAL	ARG	ARG	E	E	269 - 278	254 - 263

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.565348, 0.755805, 0.330364), (-0.748955, 0.302543, 0.589521), (0.345614, -0.580711, 0.737106)	-33.64162, 15.69523, 26.20976
3	given	(-0.136302, 0.481113, 0.865997), (-0.457655, -0.805866, 0.375675), (0.878621, -0.345122, 0.330025)	-33.0676, 60.41684, 24.77825
4	given	(-0.132149, -0.45688, 0.879657), (0.472659, -0.809096, -0.349225), (0.871281, 0.369628, 0.32287)	1.48277, 72.87045, -1.77821
5	given	(0.56369, -0.75479, 0.335478), (0.756654, 0.308982, -0.576199), (0.331252, 0.578639, 0.745285)	21.68456, 35.73824, -16.53294

#1: Protein	VP1 Mass: 29313.006 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Polyomavirus HPyV7 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D6QWK5
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 990 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.25 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 100 mM Na-Malonate pH 4.5, 15% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9795 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2010
Radiation	Monochromator: Bartels Monochromator (DCCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.7→30 Å / Num. obs: 161009 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / B_iso Wilson estimate: 26 Å² / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.7→1.75 Å / Redundancy: 3.9 % / % possible all: 82.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XDS		data scaling
PHENIX		refinement
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3S7X

3s7x

Resolution: 1.7→30 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.947 / SU B: 3.976 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19662	8094	5 %	RANDOM
R_work	0.1693	-	-	-
obs	0.17067	152915	97.78 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 24.71 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.33 Å²	0 Å²	0.35 Å²
2-	-	0.06 Å²	0 Å²
3-	-	-	-0.41 Å²

Refinement step

Cycle: 1 / Resolution: 1.7→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9689	0	36	990	10715

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.02	10133
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9541
X-RAY DIFFRACTION	r_angle_refined_deg	1.39	1.971	13872
X-RAY DIFFRACTION	r_angle_other_deg	0.759	3	21905
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.189	5	1350
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.909	23.83	423
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.132	15	1518
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.297	15	70
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	1584
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	11776
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2316
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.707	3.556	5232
X-RAY DIFFRACTION	r_mcbond_other	1.702	3.555	5231
X-RAY DIFFRACTION	r_mcangle_it	2.199	4.777	6539
X-RAY DIFFRACTION	r_mcangle_other	2.199	4.777	6540
X-RAY DIFFRACTION	r_scbond_it	2.799	4.334	4901
X-RAY DIFFRACTION	r_scbond_other	2.799	4.334	4901
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.718	5.572	7301
X-RAY DIFFRACTION	r_long_range_B_refined	6.27	10.522	11712
X-RAY DIFFRACTION	r_long_range_B_other	6.269	10.522	11712
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	1140	medium positional	0.11	0.5
B	1140	medium positional	0.12	0.5
C	1140	medium positional	0.12	0.5
D	1140	medium positional	0.1	0.5
E	1140	medium positional	0.11	0.5
A	1704	loose positional	0.34	5
B	1704	loose positional	0.36	5
C	1704	loose positional	0.35	5
D	1704	loose positional	0.31	5
E	1704	loose positional	0.41	5
A	1140	medium thermal	1.69	2
B	1140	medium thermal	1.43	2
C	1140	medium thermal	1.57	2
D	1140	medium thermal	1.59	2
E	1140	medium thermal	1.56	2
A	1704	loose thermal	2.19	10
B	1704	loose thermal	1.88	10
C	1704	loose thermal	2.43	10
D	1704	loose thermal	1.97	10
E	1704	loose thermal	2.01	10

LS refinement shell

Resolution: 1.701→1.745 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.284	458	-
R_work	0.272	9446	-
obs	-	-	81.91 %

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	1.7816	0.5906	0.033	1.1922	0.2383	1.0511	0.0484	-0.2074	0.2242	0.0549	0.0275	-0.0807	-0.2628	0.1522	-0.076	0.1007	-0.0269	0.0218	0.0944	-0.0368	0.0608	-33.6828	60.3626	-17.3035
2	1.7853	0.1645	0.3006	0.9985	0.6304	3.2681	0.0181	0.136	0.3557	-0.1898	0.0211	-0.1584	-0.3726	0.2762	-0.0392	0.1553	-0.0881	0.0375	0.1236	-0.017	0.1523	-24.4222	64.6347	-30.7313
3	0.647	0.1486	-0.1143	0.8575	0.173	1.1944	0.0234	-0.0672	0.0957	0.0428	0.0424	-0.1231	-0.1722	0.2603	-0.0658	0.0723	-0.033	0.0096	0.0972	-0.0153	0.0438	-33.5382	56.1674	-18.0057
4	0.9021	0.2266	1.006	0.5897	0.3613	3.6238	0.0288	-0.224	0.0565	0.1422	-0.0135	0.0149	0.0219	-0.2106	-0.0153	0.0806	0.0053	0.015	0.0604	-0.0103	0.0383	-48.0973	40.8741	3.0601
5	0.643	0.343	0.1319	1.4475	0.5925	1.2229	0.0145	0.0184	0.1052	-0.0263	0.0066	0.0759	-0.1607	-0.0403	-0.021	0.0262	0.0096	0.0098	0.0341	0.0072	0.0202	-49.3615	46.4252	-14.1171
6	0.4747	0.114	0.4821	0.8668	0.714	2.3157	-0.0359	-0.0179	0.0488	0.0599	0.0453	-0.0356	-0.0913	0.0641	-0.0094	0.0238	0.0024	-0.0002	0.0266	0.0012	0.0138	-45.4778	38.4765	-5.5357
7	1.1378	-0.1988	0.6837	1.1679	-0.6269	2.4183	0.1182	-0.1356	-0.2629	0.0563	-0.0334	-0.1271	0.3083	0.1709	-0.0848	0.0795	0.0169	-0.0282	0.0877	0.0234	0.1003	-37.7688	9.9142	-10.8795
8	2.4802	-0.7103	2.5651	2.7938	1.9862	6.4937	-0.1175	-0.1956	-0.0935	0.5237	0.022	-0.0734	0.2047	0.3028	0.0955	0.1419	-0.0875	-0.0914	0.3375	0.1371	0.1502	-27.9671	11.6605	3.4338
9	0.7387	0.0231	-0.0213	0.766	-0.3006	1.4219	0.0141	-0.0202	-0.0453	0.0521	-0.0184	-0.0476	0.015	0.0839	0.0043	0.0172	-0.0017	-0.0117	0.0089	-0.0009	0.0143	-41.4576	19.0687	-15.5075
10	0.5937	-0.0006	0.0657	1.6971	-0.6309	1.2534	-0.0088	0.0615	-0.2025	-0.0421	-0.0743	-0.3713	0.0987	0.4051	0.0831	0.0376	0.0347	0.0366	0.2411	-0.0087	0.1765	-14.784	22.006	-32.2264
11	3.2819	0.5209	0.9471	0.8894	-0.1172	1.8123	0.0139	0.0563	-0.358	-0.0872	-0.0585	-0.2189	0.2994	0.1907	0.0446	0.0831	0.0844	0.0209	0.1246	-0.0057	0.1452	-24.9764	8.3801	-28.7354
12	1.653	-0.0609	0.2071	1.2452	-0.366	0.8533	0.0028	-0.1002	-0.1994	0.0178	-0.0026	-0.2565	0.0708	0.2135	-0.0002	0.0337	0.0197	0.0227	0.1888	-0.008	0.1242	-17.2137	23.4441	-30.1903
13	3.9086	-0.9009	0.6534	1.0317	-0.2352	0.6027	-0.1061	0.0549	0.2469	0.0586	0.0636	-0.2209	-0.1589	0.4354	0.0425	0.1054	-0.1163	0.0344	0.3999	-0.0395	0.162	-4.887	52.7135	-30.0495
14	2.3629	0.4454	1.3934	0.8044	0.4024	2.3619	-0.0481	-0.015	0.0778	-0.0123	0.0621	-0.2435	-0.0347	0.3295	-0.014	0.0567	-0.0339	0.044	0.2545	-0.0285	0.1477	-5.5992	48.6548	-32.8009
15	1.4883	-0.0147	-0.024	0.7134	0.108	0.6599	-0.0177	-0.0127	-0.0453	-0.0707	0.0299	-0.1422	-0.0224	0.2013	-0.0122	0.0434	-0.0402	0.0409	0.1792	-0.0026	0.0566	-15.3402	43.2784	-35.9464

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	23 - 148
2	X-RAY DIFFRACTION	2	A	149 - 202
3	X-RAY DIFFRACTION	3	A	203 - 286
4	X-RAY DIFFRACTION	4	B	22 - 107
5	X-RAY DIFFRACTION	5	B	108 - 215
6	X-RAY DIFFRACTION	6	B	216 - 287
7	X-RAY DIFFRACTION	7	C	23 - 86
8	X-RAY DIFFRACTION	8	C	87 - 107
9	X-RAY DIFFRACTION	9	C	108 - 287
10	X-RAY DIFFRACTION	10	D	23 - 138
11	X-RAY DIFFRACTION	11	D	139 - 204
12	X-RAY DIFFRACTION	12	D	205 - 287
13	X-RAY DIFFRACTION	13	E	23 - 58
14	X-RAY DIFFRACTION	14	E	59 - 107
15	X-RAY DIFFRACTION	15	E	108 - 288

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+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi