PDB-28je: BKPyV VP1 IN COMPLEX WITH VHH017

ID or keywords:

Entry

Database: PDB / ID: 28je

Title

BKPyV VP1 IN COMPLEX WITH VHH017

Components

Capsid protein VP1
VHH017

Keywords

ANTIVIRAL PROTEIN / Viral capsid / BK virus / VHH

Function / homology

:

Function and homology information

Biological species

Betapolyomavirus hominis

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.492 Å

Authors

De Graef, S. / Akkermans, O. / Ubeda Nicolau, C. / Sienaert, S. / Munawar, A. / Weeks, S.D.

Funding support

1items

Citation

Journal: To Be Published
Title: Natural and patient-derived mutations in BK polyomavirus VP1 reveal structural determinants of BC-loop dependent antibody escape
Authors: Akkermans, O. / Ubeda Nicolau, C. / Bandara, A. / Correa Sierra, C. / Martins, F. / De Graef, S. / Deans, E. / Ross, S. / Sienaert, S. / Galindo Cerrada, M. / Chitalia, V. / Mani, N. / Weeks, S. / Munawar, A.

History

Deposition	Feb 3, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 26, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	28je.cif.gz	740.9 KB	Display	PDBx/mmCIF format
PDB format	pdb28je.ent.gz	602.3 KB	Display	PDB format
PDBx/mmJSON format	28je.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/8j/28je ftp://data.pdbj.org/pub/pdb/validation_reports/8j/28je	HTTPS FTP

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Related structure data

Related structure data	28jdC 28jfC C: citing same article (ref.)
Similar structure data	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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Capsid protein VP1

B: Capsid protein VP1

C: Capsid protein VP1

D: Capsid protein VP1

E: Capsid protein VP1

F: VHH017

G: VHH017

H: VHH017

I: VHH017

J: VHH017

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	85.83, 152.361, 91.933
Angle α, β, γ (deg.)	90, 94.398, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-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	1	LEU	LEU	LYS	LYS	A	A	27 - 302	3 - 272
2	1	1	LEU	LEU	LYS	LYS	B	B	27 - 296	3 - 272
3	2	2	LEU	LEU	LYS	LYS	A	A	27 - 302	3 - 272
4	2	2	LEU	LEU	LYS	LYS	C	C	27 - 296	3 - 272
5	3	3	LEU	LEU	LYS	LYS	A	A	27 - 302	3 - 272
6	3	3	LEU	LEU	LYS	LYS	D	D	27 - 296	3 - 272
7	4	4	LEU	LEU	LYS	LYS	A	A	27 - 302	3 - 272
8	4	4	LEU	LEU	LYS	LYS	E	E	27 - 296	3 - 272
9	5	5	LEU	LEU	LYS	LYS	B	B	27 - 296	3 - 272
10	5	5	LEU	LEU	LYS	LYS	C	C	27 - 296	3 - 272
11	6	6	LEU	LEU	LYS	LYS	B	B	27 - 296	3 - 272
12	6	6	LEU	LEU	LYS	LYS	D	D	27 - 296	3 - 272
13	7	7	LEU	LEU	LYS	LYS	B	B	27 - 296	3 - 272
14	7	7	LEU	LEU	LYS	LYS	E	E	27 - 296	3 - 272
15	8	8	LEU	LEU	LYS	LYS	C	C	27 - 296	3 - 272
16	8	8	LEU	LEU	LYS	LYS	D	D	27 - 296	3 - 272
17	9	9	LEU	LEU	LYS	LYS	C	C	27 - 296	3 - 272
18	9	9	LEU	LEU	LYS	LYS	E	E	27 - 296	3 - 272
19	10	10	LEU	LEU	LYS	LYS	D	D	27 - 296	3 - 272
20	10	10	LEU	LEU	LYS	LYS	E	E	27 - 296	3 - 272
21	11	11	VAL	VAL	VAL	VAL	F	F	1 - 122	2 - 123
22	11	11	VAL	VAL	VAL	VAL	G	G	1 - 122	2 - 123
23	12	12	GLU	GLU	SER	SER	F	F	0 - 123	1 - 124
24	12	12	GLU	GLU	SER	SER	H	H	0 - 123	1 - 124
25	13	13	GLU	GLU	SER	SER	F	F	0 - 123	1 - 124
26	13	13	GLU	GLU	SER	SER	I	I	0 - 123	1 - 124
27	14	14	GLU	GLU	SER	SER	F	F	0 - 123	1 - 124
28	14	14	GLU	GLU	SER	SER	J	J	0 - 123	1 - 124
29	15	15	VAL	VAL	VAL	VAL	G	G	1 - 122	2 - 123
30	15	15	VAL	VAL	VAL	VAL	H	H	1 - 122	2 - 123
31	16	16	VAL	VAL	VAL	VAL	G	G	1 - 122	2 - 123
32	16	16	VAL	VAL	VAL	VAL	I	I	1 - 122	2 - 123
33	17	17	VAL	VAL	VAL	VAL	G	G	1 - 122	2 - 123
34	17	17	VAL	VAL	VAL	VAL	J	J	1 - 122	2 - 123
35	18	18	GLU	GLU	SER	SER	H	H	0 - 123	1 - 124
36	18	18	GLU	GLU	SER	SER	I	I	0 - 123	1 - 124
37	19	19	GLU	GLU	SER	SER	H	H	0 - 123	1 - 124
38	19	19	GLU	GLU	SER	SER	J	J	0 - 123	1 - 124
39	20	20	GLU	GLU	SER	SER	I	I	0 - 123	1 - 124
40	20	20	GLU	GLU	SER	SER	J	J	0 - 123	1 - 124

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40

#1: Protein	Capsid protein VP1 Mass: 29999.803 Da / Num. of mol.: 5 / Mutation: C104S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Betapolyomavirus hominis / Strain: Dunlop / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): T7 express / References: UniProt: A0A3G2SFE7
#2: Antibody	VHH017 Mass: 14557.110 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): T7 express
#3: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 690 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.28 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion / pH: 7.5 Details: 10% w/v PEG4000, 20% v/v glycerol, 0.1M MOPS/HEPES-Na pH 7.5, 0.02 M sodium L-glutamate, 0.02M DL-alanine, 0.02M glycine, 0.02M DL-lysine HCl, 0.02M DL-serine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 18, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.49→47.3 Å / Num. obs: 81528 / % possible obs: 99.3 % / Redundancy: 3.6 % / CC_1/2: 0.99 / R_pim(I) all: 0.104 / Net I/σ(I): 6.5
Reflection shell	Resolution: 2.49→2.52 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2274 / CC_1/2: 0.29 / % possible all: 80.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.492→47.276 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.93 / SU B: 9.949 / SU ML: 0.207 / Cross valid method: FREE R-VALUE / ESU R: 0.484 / ESU R Free: 0.253
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2248	2039	2.501 %
R_work	0.1928	79489	-
all	0.194	-	-
obs	-	81528	99.246 %

Solvent computation

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

Displacement parameters

B_iso mean: 46.102 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.316 Å²	0 Å²	0.447 Å²
2-	-	0.801 Å²	-0 Å²
3-	-	-	2.418 Å²

Refinement step

Cycle: LAST / Resolution: 2.492→47.276 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14978	0	157	690	15825

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	15508
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	14357
X-RAY DIFFRACTION	r_angle_refined_deg	0.988	1.813	21008
X-RAY DIFFRACTION	r_angle_other_deg	0.358	1.751	33110
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.225	5	1939
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.268	5	96
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.669	10	2494
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.447	10	705
X-RAY DIFFRACTION	r_chiral_restr	0.048	0.2	2296
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	18492
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3618
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	2358
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	13545
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	7310
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	8066
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	644
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.024	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.136	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.228	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.348	0.2	6
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.141	4.473	7759
X-RAY DIFFRACTION	r_mcbond_other	2.141	4.474	7759
X-RAY DIFFRACTION	r_mcangle_it	3.573	8.022	9676
X-RAY DIFFRACTION	r_mcangle_other	3.574	8.023	9677
X-RAY DIFFRACTION	r_scbond_it	2.645	4.756	7749
X-RAY DIFFRACTION	r_scbond_other	2.645	4.757	7750
X-RAY DIFFRACTION	r_scangle_it	4.465	8.597	11325
X-RAY DIFFRACTION	r_scangle_other	4.464	8.598	11326
X-RAY DIFFRACTION	r_lrange_it	6.532	41.397	16053
X-RAY DIFFRACTION	r_lrange_other	6.53	41.399	16037
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.068	0.05	8138
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.065	0.05	8050
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.063	0.05	8094
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.068	0.05	8129
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.061	0.05	8115
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.058	0.05	8163
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.066	0.05	8109
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.068	0.05	8072
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.059	0.05	8018
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.057	0.05	8079
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.067	0.05	3795
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.076	0.05	3857
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.07	0.05	3833
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.049	0.05	3872
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.072	0.05	3786
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.038	0.05	3833
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.057	0.05	3822
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.073	0.05	3837
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.072	0.05	3851
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.055	0.05	3882

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06816	0.05011
1	2	B	X-RAY DIFFRACTION	Local ncs	0.06816	0.05011
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06526	0.05011
2	4	C	X-RAY DIFFRACTION	Local ncs	0.06526	0.05011
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06335	0.05011
3	6	D	X-RAY DIFFRACTION	Local ncs	0.06335	0.05011
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06801	0.05011
4	8	E	X-RAY DIFFRACTION	Local ncs	0.06801	0.05011
5	9	B	X-RAY DIFFRACTION	Local ncs	0.06053	0.05011
5	10	C	X-RAY DIFFRACTION	Local ncs	0.06053	0.05011
6	11	B	X-RAY DIFFRACTION	Local ncs	0.05807	0.05011
6	12	D	X-RAY DIFFRACTION	Local ncs	0.05807	0.05011
7	13	B	X-RAY DIFFRACTION	Local ncs	0.06639	0.0501
7	14	E	X-RAY DIFFRACTION	Local ncs	0.06639	0.0501
8	15	C	X-RAY DIFFRACTION	Local ncs	0.06753	0.05011
8	16	D	X-RAY DIFFRACTION	Local ncs	0.06753	0.05011
9	17	C	X-RAY DIFFRACTION	Local ncs	0.05861	0.0501
9	18	E	X-RAY DIFFRACTION	Local ncs	0.05861	0.0501
10	19	D	X-RAY DIFFRACTION	Local ncs	0.05748	0.05011
10	20	E	X-RAY DIFFRACTION	Local ncs	0.05748	0.05011
11	21	F	X-RAY DIFFRACTION	Local ncs	0.06654	0.05011
11	22	G	X-RAY DIFFRACTION	Local ncs	0.06654	0.05011
12	23	F	X-RAY DIFFRACTION	Local ncs	0.07597	0.05012
12	24	H	X-RAY DIFFRACTION	Local ncs	0.07597	0.05012
13	25	F	X-RAY DIFFRACTION	Local ncs	0.06963	0.05011
13	26	I	X-RAY DIFFRACTION	Local ncs	0.06963	0.05011
14	27	F	X-RAY DIFFRACTION	Local ncs	0.04861	0.05012
14	28	J	X-RAY DIFFRACTION	Local ncs	0.04861	0.05012
15	29	G	X-RAY DIFFRACTION	Local ncs	0.07183	0.05011
15	30	H	X-RAY DIFFRACTION	Local ncs	0.07183	0.05011
16	31	G	X-RAY DIFFRACTION	Local ncs	0.0382	0.05011
16	32	I	X-RAY DIFFRACTION	Local ncs	0.0382	0.05011
17	33	G	X-RAY DIFFRACTION	Local ncs	0.05696	0.05011
17	34	J	X-RAY DIFFRACTION	Local ncs	0.05696	0.05011
18	35	H	X-RAY DIFFRACTION	Local ncs	0.07269	0.05011
18	36	I	X-RAY DIFFRACTION	Local ncs	0.07269	0.05011
19	37	H	X-RAY DIFFRACTION	Local ncs	0.07237	0.05011
19	38	J	X-RAY DIFFRACTION	Local ncs	0.07237	0.05011
20	39	I	X-RAY DIFFRACTION	Local ncs	0.05502	0.05011
20	40	J	X-RAY DIFFRACTION	Local ncs	0.05502	0.05011

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.492-2.556	0.376	211	0.33	5246	0.331	6054	0.917	0.934	90.1387	0.317
2.556-2.626	0.322	140	0.312	5760	0.312	5900	0.934	0.944	100	0.293
2.626-2.702	0.339	132	0.275	5587	0.276	5719	0.936	0.955	100	0.253
2.702-2.785	0.297	133	0.266	5437	0.267	5570	0.95	0.96	100	0.24
2.785-2.876	0.256	136	0.235	5270	0.236	5406	0.956	0.968	100	0.205
2.876-2.976	0.215	131	0.212	5056	0.212	5187	0.968	0.973	100	0.188
2.976-3.088	0.264	113	0.198	4941	0.199	5055	0.953	0.975	99.9802	0.174
3.088-3.214	0.212	123	0.19	4694	0.19	4818	0.972	0.978	99.9792	0.169
3.214-3.356	0.221	110	0.19	4583	0.191	4694	0.97	0.98	99.9787	0.17
3.356-3.519	0.197	109	0.182	4331	0.182	4440	0.977	0.983	100	0.165
3.519-3.708	0.223	109	0.181	4138	0.182	4247	0.971	0.982	100	0.165
3.708-3.931	0.163	96	0.171	3900	0.171	3997	0.983	0.984	99.975	0.157
3.931-4.201	0.213	86	0.159	3706	0.16	3793	0.973	0.986	99.9736	0.148
4.201-4.534	0.177	79	0.14	3434	0.141	3513	0.98	0.988	100	0.134
4.534-4.963	0.184	80	0.138	3142	0.139	3222	0.982	0.989	100	0.133
4.963-5.541	0.181	72	0.163	2874	0.164	2946	0.984	0.987	100	0.16
5.541-6.383	0.244	63	0.217	2537	0.218	2601	0.973	0.979	99.9616	0.207
6.383-7.783	0.234	54	0.19	2169	0.191	2224	0.975	0.981	99.955	0.183
7.783-10.86	0.204	37	0.171	1698	0.171	1735	0.973	0.982	100	0.173
10.86-47.276	0.236	25	0.267	986	0.266	1014	0.973	0.957	99.7041	0.271

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-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