PDB-28jd: BKPyV VP1 IN COMPLEX WITH scFv 319C07

ID or keywords:

Entry

Database: PDB / ID: 28jd

Title

BKPyV VP1 IN COMPLEX WITH scFv 319C07

Components

319C07 scFv
Capsid protein VP1

Keywords

ANTIVIRAL PROTEIN / Viral capsid / BK virus / scFv

Function / homology

:

Function and homology information

Biological species

Betapolyomavirus hominis

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.726 Å

Authors

Ubeda Nicolau, C. / Akkermans, O. / Sienaert, S. / De Graef, 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	28jd.cif.gz	397.8 KB	Display	PDBx/mmCIF format
PDB format	pdb28jd.ent.gz	316.2 KB	Display	PDB format
PDBx/mmJSON format	28jd.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/28jd ftp://data.pdbj.org/pub/pdb/validation_reports/8j/28jd	HTTPS FTP

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Related structure data

Related structure data	28jeC 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: 319C07 scFv

G: 319C07 scFv

H: 319C07 scFv

233 kDa, 8 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)	110.25, 151.89, 164.69
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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	ILE	ILE	LYS	LYS	A	A	28 - 296	4 - 272
2	1	1	ILE	ILE	LYS	LYS	B	B	28 - 296	4 - 272
3	2	2	ILE	ILE	VAL	VAL	A	A	28 - 295	4 - 271
4	2	2	ILE	ILE	VAL	VAL	C	C	28 - 295	4 - 271
5	3	3	ILE	ILE	LYS	LYS	A	A	28 - 296	4 - 272
6	3	3	ILE	ILE	LYS	LYS	D	D	28 - 296	4 - 272
7	4	4	ILE	ILE	LYS	LYS	A	A	28 - 296	4 - 272
8	4	4	ILE	ILE	LYS	LYS	E	E	28 - 296	4 - 272
9	5	5	ILE	ILE	VAL	VAL	B	B	28 - 295	4 - 271
10	5	5	ILE	ILE	VAL	VAL	C	C	28 - 295	4 - 271
11	6	6	ILE	ILE	LYS	LYS	B	B	28 - 296	4 - 272
12	6	6	ILE	ILE	LYS	LYS	D	D	28 - 296	4 - 272
13	7	7	ILE	ILE	LYS	LYS	B	B	28 - 296	4 - 272
14	7	7	ILE	ILE	LYS	LYS	E	E	28 - 296	4 - 272
15	8	8	ILE	ILE	VAL	VAL	C	C	28 - 295	4 - 271
16	8	8	ILE	ILE	VAL	VAL	D	D	28 - 295	4 - 271
17	9	9	ILE	ILE	VAL	VAL	C	C	28 - 295	4 - 271
18	9	9	ILE	ILE	VAL	VAL	E	E	28 - 295	4 - 271
19	10	10	ILE	ILE	LYS	LYS	D	D	28 - 296	4 - 272
20	10	10	ILE	ILE	LYS	LYS	E	E	28 - 296	4 - 272
21	11	11	GLU	GLU	SER	SER	F	F	2 - 250	2 - 250
22	11	11	GLU	GLU	SER	SER	G	G	1 - 250	2 - 250
23	12	12	GLU	GLU	VAL	VAL	F	F	2 - 249	2 - 249
24	12	12	GLU	GLU	VAL	VAL	H	H	1 - 249	2 - 249
25	13	13	GLU	GLU	SER	SER	G	G	1 - 251	2 - 251
26	13	13	GLU	GLU	SER	SER	H	H	1 - 251	2 - 251

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

#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	319C07 scFv Mass: 27658.629 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): T7 Express
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: 2.96 Å³/Da / Density % sol: 58.44 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion / pH: 9 / Details: 10% (w/v) PEG 6,000 100 mM Bicine pH 9.0

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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: Feb 13, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 3.7→111.904 Å / Num. obs: 29566 / % possible obs: 99.9 % / Redundancy: 8.5 % / CC_1/2: 1 / R_pim(I) all: 0.023 / Net I/σ(I): 3.7
Reflection shell	Resolution: 3.77→3.79 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1460 / CC_1/2: 0.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
autoPROC		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.726→111.904 Å / Cor.coef. F_o:F_c: 0.828 / Cor.coef. F_o:F_c free: 0.866 / SU B: 60.418 / SU ML: 0.785 / Cross valid method: THROUGHOUT / ESU R Free: 0.824
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2941	1475	4.99 %	RANDOM
R_work	0.2463	28087	-	-
all	0.249	-	-	-
obs	-	29562	99.929 %	-

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: 120.484 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	11.218 Å²	0 Å²	0 Å²
2-	-	-3.154 Å²	0 Å²
3-	-	-	-8.064 Å²

Refinement step

Cycle: LAST / Resolution: 3.726→111.904 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15393	0	0	0	15393

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	15707
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	14428
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.035	0.1	210804
X-RAY DIFFRACTION	r_angle_refined_deg	1.245	1.81	21372
X-RAY DIFFRACTION	r_angle_other_deg	0.468	1.739	33277
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.999	5	1972
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.203	5	87
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.841	10	2475
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.106	10	682
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	2359
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	18675
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3637
X-RAY DIFFRACTION	r_nbd_refined	0.185	0.2	2333
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	13163
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	7380
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	7976
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.122	0.2	251
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.197	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.323	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.302	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.588	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	5.783	12.113	7939
X-RAY DIFFRACTION	r_mcbond_other	5.781	12.113	7939
X-RAY DIFFRACTION	r_mcangle_it	9.512	21.813	9894
X-RAY DIFFRACTION	r_mcangle_other	9.512	21.813	9895
X-RAY DIFFRACTION	r_scbond_it	5.247	12.352	7768
X-RAY DIFFRACTION	r_scbond_other	5.246	12.353	7769
X-RAY DIFFRACTION	r_scangle_it	8.882	22.648	11478
X-RAY DIFFRACTION	r_scangle_other	8.882	22.648	11479
X-RAY DIFFRACTION	r_lrange_it	15.883	274.791	213869
X-RAY DIFFRACTION	r_lrange_other	15.883	274.79	213870
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.08	0.05	7911
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.065	0.05	7930
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.074	0.05	7994
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.063	0.05	7837
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.072	0.05	7911
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.077	0.05	7942
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.056	0.05	7892
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.061	0.05	7958
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.052	0.05	7894
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.057	0.05	7874
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.076	0.05	6940
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.079	0.05	6949
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.063	0.05	6994

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	0.08036	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08036	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06467	0.0501
2	4	C	X-RAY DIFFRACTION	Local ncs	0.06467	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07425	0.0501
3	6	D	X-RAY DIFFRACTION	Local ncs	0.07425	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06341	0.0501
4	8	E	X-RAY DIFFRACTION	Local ncs	0.06341	0.0501
5	9	B	X-RAY DIFFRACTION	Local ncs	0.07174	0.0501
5	10	C	X-RAY DIFFRACTION	Local ncs	0.07174	0.0501
6	11	B	X-RAY DIFFRACTION	Local ncs	0.07739	0.0501
6	12	D	X-RAY DIFFRACTION	Local ncs	0.07739	0.0501
7	13	B	X-RAY DIFFRACTION	Local ncs	0.05632	0.0501
7	14	E	X-RAY DIFFRACTION	Local ncs	0.05632	0.0501
8	15	C	X-RAY DIFFRACTION	Local ncs	0.06148	0.0501
8	16	D	X-RAY DIFFRACTION	Local ncs	0.06148	0.0501
9	17	C	X-RAY DIFFRACTION	Local ncs	0.05225	0.05011
9	18	E	X-RAY DIFFRACTION	Local ncs	0.05225	0.05011
10	19	D	X-RAY DIFFRACTION	Local ncs	0.05678	0.0501
10	20	E	X-RAY DIFFRACTION	Local ncs	0.05678	0.0501
11	21	F	X-RAY DIFFRACTION	Local ncs	0.07619	0.05011
11	22	G	X-RAY DIFFRACTION	Local ncs	0.07619	0.05011
12	23	F	X-RAY DIFFRACTION	Local ncs	0.07914	0.0501
12	24	H	X-RAY DIFFRACTION	Local ncs	0.07914	0.0501
13	25	G	X-RAY DIFFRACTION	Local ncs	0.06266	0.05011
13	26	H	X-RAY DIFFRACTION	Local ncs	0.06266	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
3.726-3.823	0.356	114	0.385	2041	0.383	2158	0.895	0.852	99.861	0.379
3.823-3.927	0.33	91	0.335	2006	0.335	2098	0.919	0.898	99.9523	0.327
3.927-4.041	0.331	105	0.308	1930	0.309	2035	0.917	0.919	100	0.298
4.041-4.165	0.338	90	0.284	1894	0.287	1985	0.908	0.932	99.9496	0.271
4.165-4.302	0.282	114	0.252	1806	0.254	1920	0.943	0.95	100	0.239
4.302-4.452	0.256	81	0.218	1778	0.219	1861	0.957	0.963	99.8925	0.201
4.452-4.62	0.324	87	0.213	1734	0.218	1821	0.934	0.966	100	0.197
4.62-4.809	0.244	101	0.201	1628	0.204	1729	0.957	0.971	100	0.183
4.809-5.022	0.303	83	0.209	1571	0.214	1654	0.94	0.968	100	0.192
5.022-5.266	0.298	67	0.215	1541	0.219	1608	0.939	0.969	100	0.201
5.266-5.551	0.263	81	0.213	1442	0.216	1523	0.957	0.97	100	0.196
5.551-5.886	0.319	63	0.211	1385	0.216	1449	0.948	0.972	99.931	0.197
5.886-6.292	0.336	69	0.219	1295	0.224	1364	0.952	0.972	100	0.204
6.292-6.794	0.272	65	0.211	1212	0.214	1277	0.948	0.973	100	0.197
6.794-7.44	0.264	60	0.19	1125	0.193	1185	0.957	0.976	100	0.181
7.44-8.313	0.273	59	0.191	1016	0.195	1076	0.951	0.975	99.9071	0.182
8.313-9.59	0.253	54	0.195	907	0.198	961	0.967	0.976	100	0.191
9.59-11.724	0.242	42	0.208	786	0.21	828	0.966	0.977	100	0.206
11.724-16.491	0.309	33	0.269	619	0.271	653	0.93	0.959	99.8469	0.271
16.491-111.904	0.4	16	0.523	371	0.518	398	0.922	0.808	97.2362	0.977

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