PDB-3s7v: Unassembled KI Polyomavirus VP1 Pentamer

ID or keywords:

Entry

Database: PDB / ID: 3s7v

Title

Unassembled KI Polyomavirus VP1 Pentamer

Components

Major capsid protein VP1

Keywords

VIRAL PROTEIN / jelly-roll / antiparallel beta sandwich / major capsid protein

Function / homology

Function and homology information

T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function

Biological species

KI polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Neu, U. / Stehle, T.

Citation

Journal: J.Virol. / Year: 2011
Title: Structures of the major capsid proteins of the human KI and WU polyomaviruses.
Authors: Neu, U. / Wang, J. / Macejak, D. / Garcea, R.L. / Stehle, T.

History

Deposition	May 27, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 29, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3s7v.cif.gz	994.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3s7v.ent.gz	837.7 KB	Display	PDB format
PDBx/mmJSON format	3s7v.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/s7/3s7v ftp://data.pdbj.org/pub/pdb/validation_reports/s7/3s7v	HTTPS FTP

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Related structure data

Related structure data	3s7xC 1vps 3bwr 3nxg C: citing same article (ref.)
Similar structure data	4fmi-1 4pot-1 4fmh-1 3bwr-d 4u61-1 5cpz-d 4fmi-3 4fmh-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 (5)

Deposited unit

A: Major capsid protein VP1

B: Major capsid protein VP1

C: Major capsid protein VP1

D: Major capsid protein VP1

E: Major capsid protein VP1

F: Major capsid protein VP1

G: Major capsid protein VP1

H: Major capsid protein VP1

I: Major capsid protein VP1

J: Major capsid protein VP1

303 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Major capsid protein VP1

B: Major capsid protein VP1

C: Major capsid protein VP1

D: Major capsid protein VP1

E: Major capsid protein VP1

defined by author&software
152 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Major capsid protein VP1

G: Major capsid protein VP1

H: Major capsid protein VP1

I: Major capsid protein VP1

J: Major capsid protein VP1

defined by author&software
152 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.330, 82.780, 142.060
Angle α, β, γ (deg.)	87.01, 98.23, 108.65
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	A	46 - 62
2	1	1	3	B	46 - 62
3	1	1	3	C	46 - 62
4	1	1	3	D	46 - 62
5	1	1	3	E	46 - 62
6	1	1	3	F	46 - 62
7	1	1	3	G	46 - 62
8	1	1	3	H	46 - 62
9	1	1	3	I	46 - 62
10	1	1	3	J	46 - 62
1	2	1	3	A	69 - 82
2	2	1	3	B	69 - 82
3	2	1	3	C	69 - 82
4	2	1	3	D	69 - 82
5	2	1	3	E	69 - 82
6	2	1	3	F	69 - 82
7	2	1	3	G	69 - 82
8	2	1	3	H	69 - 82
9	2	1	3	I	69 - 82
10	2	1	3	J	69 - 82
1	3	1	3	A	90 - 114
2	3	1	3	B	90 - 114
3	3	1	3	C	90 - 114
4	3	1	3	D	90 - 114
5	3	1	3	E	90 - 114
6	3	1	3	F	90 - 114
7	3	1	3	G	90 - 114
8	3	1	3	H	90 - 114
9	3	1	3	I	90 - 114
10	3	1	3	J	90 - 114
1	4	1	3	A	124 - 146
2	4	1	3	B	124 - 146
3	4	1	3	C	124 - 146
4	4	1	3	D	124 - 146
5	4	1	3	E	124 - 146
6	4	1	3	F	124 - 146
7	4	1	3	G	124 - 146
8	4	1	3	H	124 - 146
9	4	1	3	I	124 - 146
10	4	1	3	J	124 - 146
1	5	1	6	A	231 - 233
2	5	1	6	B	231 - 233
3	5	1	6	C	231 - 233
4	5	1	6	D	231 - 233
5	5	1	6	E	231 - 233
6	5	1	6	F	231 - 233
7	5	1	6	G	231 - 233
8	5	1	6	H	231 - 233
9	5	1	6	I	231 - 233
10	5	1	6	J	231 - 233
1	6	1	3	A	235 - 300
2	6	1	3	B	235 - 300
3	6	1	3	C	235 - 300
4	6	1	3	D	235 - 300
5	6	1	3	E	235 - 300
6	6	1	3	F	235 - 300
7	6	1	3	G	235 - 300
8	6	1	3	H	235 - 300
9	6	1	3	I	235 - 300
10	6	1	3	J	235 - 300
1	7	1	5	A	42 - 44
2	7	1	5	B	42 - 44
3	7	1	5	C	42 - 44
4	7	1	5	D	42 - 44
5	7	1	5	E	42 - 44
6	7	1	5	F	42 - 44
7	7	1	5	G	42 - 44
8	7	1	5	H	42 - 44
9	7	1	5	I	42 - 44
10	7	1	5	J	42 - 44
1	8	1	3	A	205 - 229
2	8	1	3	B	205 - 229
3	8	1	3	C	205 - 229
4	8	1	3	D	205 - 229
5	8	1	3	E	205 - 229
6	8	1	3	F	205 - 229
7	8	1	3	G	205 - 229
8	8	1	3	H	205 - 229
9	8	1	3	I	205 - 229
10	8	1	3	J	205 - 229
1	9	1	3	A	151 - 201
2	9	1	3	B	151 - 201
3	9	1	3	C	151 - 201
4	9	1	3	D	151 - 201
5	9	1	3	E	151 - 201
6	9	1	3	F	151 - 201
7	9	1	3	G	151 - 201
8	9	1	3	H	151 - 201
9	9	1	3	I	151 - 201
10	9	1	3	J	151 - 201
1	10	1	3	A	33 - 41
2	10	1	3	B	33 - 41
3	10	1	3	C	33 - 41
4	10	1	3	D	33 - 41
5	10	1	3	E	33 - 41
6	10	1	3	F	33 - 41
7	10	1	3	G	33 - 41
8	10	1	3	H	33 - 41
9	10	1	3	I	33 - 41
10	10	1	3	J	33 - 41
1	1	2	5	A	83 - 89
2	1	2	5	C	83 - 89
3	1	2	5	D	83 - 89
4	1	2	5	E	83 - 89
5	1	2	5	F	83 - 89
6	1	2	5	I	83 - 89
7	1	2	5	J	83 - 89

NCS ensembles :

ID
1
2

#1: Protein	Major capsid protein VP1 / / Major structural protein VP1 Mass: 30309.129 Da / Num. of mol.: 10 / Fragment: UNP residues 32-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KI polyomavirus / Gene: VP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3R4N3, UniProt: P0DOI2*PLUS
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Major capsid protein VP1 /

/ Major structural protein VP1

Mass: 30309.129 Da / Num. of mol.: 10 / Fragment: UNP residues 32-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

KI polyomavirus / Gene: VP1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3R4N3, UniProt: P0DOI2*PLUS

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.56 Å³/Da / Density % sol: 51.93 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M sodium formate pH 7.0, 20 % (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2009
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.55→50 Å / Num. all: 98003 / Num. obs: 93982 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / R_merge(I) obs: 0.054 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.55→2.62 Å / R_merge(I) obs: 0.602 / Mean I/σ(I) obs: 1.4 / % possible all: 91.1

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Processing

Software

Name	Version	Classification
RemDAq		data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→49.27 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.942 / SU B: 23.626 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.852 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21939	4647	4.9 %	RANDOM
R_work	0.20247	-	-	-
obs	0.20332	89331	95.93 %	-
all	-	93982	-	-

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: 61.899 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.81 Å²	0.37 Å²	-0.19 Å²
2-	-	-1.25 Å²	-0.12 Å²
3-	-	-	-1.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→49.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20226	0	0	117	20343

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	20737
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.252	1.963	28355
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.172	5	2587
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.035	23.732	879
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.688	15	3194
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.025	15	135
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	3227
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.022	15915
X-RAY DIFFRACTION	r_gen_planes_other
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	1.154	5	13081
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.902	8	21350
X-RAY DIFFRACTION	r_scbond_it	1.745	5	7656
X-RAY DIFFRACTION	r_scangle_it	2.701	8	7005
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	908	tight positional	0.03	0.05
1	2	B	908	tight positional	0.03	0.05
1	3	C	908	tight positional	0.03	0.05
1	4	D	908	tight positional	0.02	0.05
1	5	E	908	tight positional	0.02	0.05
1	6	F	908	tight positional	0.03	0.05
1	7	G	908	tight positional	0.03	0.05
1	8	H	908	tight positional	0.03	0.05
1	9	I	908	tight positional	0.03	0.05
1	10	J	908	tight positional	0.03	0.05
1	1	A	8	medium positional	0.02	0.5
1	2	B	8	medium positional	0.03	0.5
1	3	C	8	medium positional	0.07	0.5
1	4	D	8	medium positional	0.02	0.5
1	5	E	8	medium positional	0.02	0.5
1	6	F	8	medium positional	0.05	0.5
1	7	G	8	medium positional	0.04	0.5
1	8	H	8	medium positional	0.03	0.5
1	9	I	8	medium positional	0.02	0.5
1	10	J	8	medium positional	0.03	0.5
2	1	A	24	medium positional	0.09	0.5
2	2	C	24	medium positional	0.25	0.5
2	3	D	24	medium positional	0.2	0.5
2	4	E	24	medium positional	0.18	0.5
2	5	F	24	medium positional	0.24	0.5
2	6	I	24	medium positional	0.12	0.5
2	7	J	24	medium positional	0.17	0.5
1	1	A	883	loose positional	0.03	5
1	2	B	883	loose positional	0.03	5
1	3	C	883	loose positional	0.03	5
1	4	D	883	loose positional	0.03	5
1	5	E	883	loose positional	0.03	5
1	6	F	883	loose positional	0.03	5
1	7	G	883	loose positional	0.03	5
1	8	H	883	loose positional	0.03	5
1	9	I	883	loose positional	0.03	5
1	10	J	883	loose positional	0.03	5
2	1	A	18	loose positional	0.36	5
2	2	C	18	loose positional	0.51	5
2	3	D	18	loose positional	0.62	5
2	4	E	18	loose positional	0.29	5
2	5	F	18	loose positional	0.63	5
2	6	I	18	loose positional	0.3	5
2	7	J	18	loose positional	0.46	5
1	1	A	908	tight thermal	0.06	0.5
1	2	B	908	tight thermal	0.07	0.5
1	3	C	908	tight thermal	0.07	0.5
1	4	D	908	tight thermal	0.06	0.5
1	5	E	908	tight thermal	0.06	0.5
1	6	F	908	tight thermal	0.07	0.5
1	7	G	908	tight thermal	0.07	0.5
1	8	H	908	tight thermal	0.07	0.5
1	9	I	908	tight thermal	0.08	0.5
1	10	J	908	tight thermal	0.07	0.5
1	1	A	8	medium thermal	0.03	2
1	2	B	8	medium thermal	0.07	2
1	3	C	8	medium thermal	0.06	2
1	4	D	8	medium thermal	0.02	2
1	5	E	8	medium thermal	0.03	2
1	6	F	8	medium thermal	0.04	2
1	7	G	8	medium thermal	0.01	2
1	8	H	8	medium thermal	0.05	2
1	9	I	8	medium thermal	0.03	2
1	10	J	8	medium thermal	0.02	2
2	1	A	24	medium thermal	0.41	2
2	2	C	24	medium thermal	0.44	2
2	3	D	24	medium thermal	0.55	2
2	4	E	24	medium thermal	0.42	2
2	5	F	24	medium thermal	0.39	2
2	6	I	24	medium thermal	0.45	2
2	7	J	24	medium thermal	0.57	2
1	1	A	883	loose thermal	0.06	10
1	2	B	883	loose thermal	0.06	10
1	3	C	883	loose thermal	0.07	10
1	4	D	883	loose thermal	0.06	10
1	5	E	883	loose thermal	0.06	10
1	6	F	883	loose thermal	0.06	10
1	7	G	883	loose thermal	0.06	10
1	8	H	883	loose thermal	0.06	10
1	9	I	883	loose thermal	0.06	10
1	10	J	883	loose thermal	0.07	10
2	1	A	18	loose thermal	0.53	10
2	2	C	18	loose thermal	0.52	10
2	3	D	18	loose thermal	0.46	10
2	4	E	18	loose thermal	0.42	10
2	5	F	18	loose thermal	0.55	10
2	6	I	18	loose thermal	0.71	10
2	7	J	18	loose thermal	0.72	10

LS refinement shell

Resolution: 2.55→2.616 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.387	304	-
R_work	0.348	6318	-
obs	-	-	91.19 %

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	0.7536	-0.1114	0.1003	0.8786	-0.0346	2.1431	-0.1051	0.0298	0.0549	-0.1137	0.0369	-0.086	-0.6274	0.1124	0.0681	0.4407	-0.0069	-0.0091	0.2065	0.0047	0.1636	-26.48	40.76	-17.111
2	1.1152	0.2385	0.328	1.1218	0.2378	1.8663	-0.0394	-0.0464	0.0789	-0.0381	0.0024	0.0621	-0.5241	-0.2641	0.0369	0.3699	0.1299	0.0518	0.1978	-0.0013	0.1428	-33.404	40.129	11.996
3	0.9464	0.0155	0.6147	0.7602	0.0087	1.8462	0.0919	-0.1305	-0.1243	0.1362	0.0325	0.0524	0.0517	-0.277	-0.1245	0.2043	-0.0597	0.0224	0.1938	0.0361	0.2064	-30.307	11.981	21.608
4	0.618	-0.1751	0.5091	1.3359	-0.5902	2.2631	0.1898	0.0621	-0.2061	-0.029	-0.0407	-0.0368	0.5102	0.1651	-0.149	0.3865	-0.0019	-0.0998	0.165	-0.058	0.2904	-23.233	-4.85	-2.296
5	0.8167	-0.3132	0.364	1.3437	-0.1736	1.962	0.1111	0.1935	-0.0817	-0.1871	-0.0498	-0.1218	0.2356	0.3784	-0.0613	0.29	0.0519	-0.0034	0.2916	-0.0821	0.1843	-19.953	13.146	-25.922
6	1.4186	-0.0901	-0.5469	1.2379	0.2452	1.4894	-0.1855	-0.2752	-0.1354	0.071	0.033	0.0004	0.3844	0.1592	0.1524	0.3073	0.1197	-0.0283	0.192	0.0491	0.1409	-15.363	29.177	-57.351
7	1.2943	0.4495	-0.6147	1.4977	-0.4337	2.0408	0.1011	-0.3811	0.2979	0.2928	0.0804	0.132	-0.0705	0.2058	-0.1815	0.2088	0.004	-0.0325	0.2308	-0.1429	0.2363	-18.723	57.719	-49.019
8	1.1034	-0.3278	-0.4191	1.2222	-0.0425	1.4007	0.1769	-0.0755	0.3257	0.1495	0.0632	0.188	-0.2948	-0.0419	-0.24	0.1977	-0.0374	0.0751	0.076	-0.0123	0.4514	-20.104	74.853	-73.511
9	0.9479	-0.3675	-0.2874	1.547	-0.2462	1.2633	0.0201	0.158	0.1682	-0.2426	0.0908	0.119	-0.008	-0.187	-0.111	0.1993	-0.0228	-0.03	0.1383	0.0759	0.2314	-15.833	56.573	-96.868
10	0.9015	-0.0382	-0.196	1.0266	-0.1461	1.7209	-0.175	0.0434	-0.1316	-0.2236	0.0779	0.0449	0.3513	-0.0877	0.0972	0.351	0.0001	0.0099	0.087	0.0015	0.1535	-13.972	28.641	-87.27

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	35 - 304
2	X-RAY DIFFRACTION	2	B	35 - 303
3	X-RAY DIFFRACTION	3	C	34 - 304
4	X-RAY DIFFRACTION	4	D	34 - 304
5	X-RAY DIFFRACTION	5	E	35 - 304
6	X-RAY DIFFRACTION	6	F	30 - 304
7	X-RAY DIFFRACTION	7	G	35 - 304
8	X-RAY DIFFRACTION	8	H	34 - 303
9	X-RAY DIFFRACTION	9	I	36 - 304
10	X-RAY DIFFRACTION	10	J	35 - 304

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