9RM2 | pdb_00009rm2

BKPyV VP1 IN COMPLEX WITH 319C07-FAB

PDB DOI: https://doi.org/10.2210/pdb9RM2/pdb

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens, Betapolyomavirus hominis
Expression System: Cricetulus griseus, Escherichia coli
Mutation(s): Yes

Deposited: 2025-06-17 Released: 2025-07-09
Deposition Author(s): Schmitt, S., Hillenbrand, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.218 (Depositor), 0.223 (DCC)
R-Value Work:
0.187 (Depositor), 0.193 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A highly potent human antibody neutralizing all serotypes of BK polyomavirus.

Weber, M., Schmitt, S., Eicher, B., Seidenberg, J., Rutkauskaite, J., Stockli, B., Townsend, C., Huynh-Do, U., Schachtner, T., Delbue, S., Mader, A., Esslinger, C., Hillenbrand, M.

(2025) PLoS Pathog 21: e1013122-e1013122

PubMed: 40680077 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1013122
Primary Citation of Related Structures:
9RM2

PubMed Abstract:
BK polyomavirus infection poses a significant risk to kidney transplant recipients. Reactivation of dormant virus in the transplanted kidney, triggered by immunosuppression, can lead to BK polyomavirus-associated nephropathy in up to 10% of transplants, often resulting in loss of graft function or even graft loss. Currently, there is no specific treatment that reliably prevents BK polyomavirus-associated nephropathy or halts its progression. Standard of care relies on reducing immunosuppression, allowing the immune system to gradually control the infection but at the risk of provoking rejection episodes and compromising kidney function. This study describes the discovery and characterization of a highly-potent BK polyomavirus-neutralizing antibody, identified from a kidney transplant recipient who displayed rapid clearance of high-level BKPyV-DNAemia. Antibody mAb 319C07 (USAN potravitug) neutralizes all four BK polyomavirus serotypes and recognizes an epitope critical for viral cell attachment. mAb 319C07 is in clinical development for the treatment of BKPyV infection in renal transplant patients (NCT05769582).

Organizational Affiliation

Memo Therapeutics AG, Schlieren Zurich, Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 408.45 kDa
Atom Count: 29,832
Modeled Residue Count: 3,522
Deposited Residue Count: 3,690
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
319C07 antibody heavy chain, Fab fragment	A [auth H], D [auth A], G [auth D], J [auth G], M	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
319C07 antibody light chain, Fab fragment	B [auth L], E [auth B], H [auth E], K [auth J], N	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein VP1	C [auth P], F [auth C], I [auth F], L [auth K], O	300	Betapolyomavirus hominis	Mutation(s): 4
UniProt
Find proteins for P03088 (BK polyomavirus) Explore P03088 Go to UniProtKB: P03088
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03088
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain BB [auth J] MOL2 format, chain BB [auth J] mmCIF format, chain BB [auth J]	BB [auth J]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain BB [auth J] Interactions & Density Focus chain BB [auth J]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain WA [auth G] MOL2 format, chain WA [auth G] mmCIF format, chain WA [auth G]	WA [auth G]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain WA [auth G] Interactions & Density Focus chain WA [auth G]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain LB [auth M] SDF format, chain RB [auth N] SDF format, chain SB [auth N] SDF format, chain U [auth L] SDF format, chain X [auth P] MOL2 format, chain BA [auth B] MOL2 format, chain LB [auth M] MOL2 format, chain RB [auth N] MOL2 format, chain SB [auth N] MOL2 format, chain U [auth L] MOL2 format, chain X [auth P] mmCIF format, chain BA [auth B] mmCIF format, chain LB [auth M] mmCIF format, chain RB [auth N] mmCIF format, chain SB [auth N] mmCIF format, chain U [auth L] mmCIF format, chain X [auth P]	BA [auth B] LB [auth M] RB [auth N] SB [auth N] U [auth L] BA [auth B], LB [auth M], RB [auth N], SB [auth N], U [auth L], X [auth P]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain LB [auth M] Focus chain RB [auth N] Focus chain SB [auth N] Focus chain U [auth L] Focus chain X [auth P] Interactions & Density Focus chain BA [auth B] Focus chain LB [auth M] Focus chain RB [auth N] Focus chain SB [auth N] Focus chain U [auth L] Focus chain X [auth P]
PG5 Query on PG5 Download Ideal Coordinates CCD File SDF format, chain V [auth L] SDF format, chain YA [auth J] MOL2 format, chain V [auth L] MOL2 format, chain YA [auth J] mmCIF format, chain V [auth L] mmCIF format, chain YA [auth J]	V [auth L], YA [auth J]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain V [auth L] Focus chain YA [auth J] Interactions & Density Focus chain V [auth L] Focus chain YA [auth J]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain JA [auth C] SDF format, chain MB [auth M] SDF format, chain Q [auth H] SDF format, chain R [auth H] SDF format, chain RA [auth E] SDF format, chain Y [auth P] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain MB [auth M] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth H] MOL2 format, chain RA [auth E] MOL2 format, chain Y [auth P] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain MB [auth M] mmCIF format, chain Q [auth H] mmCIF format, chain R [auth H] mmCIF format, chain RA [auth E] mmCIF format, chain Y [auth P]	CA [auth B] DA [auth B] EA [auth B] JA [auth C] MB [auth M] CA [auth B], DA [auth B], EA [auth B], JA [auth C], MB [auth M], Q [auth H], R [auth H], RA [auth E], Y [auth P]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain JA [auth C] Focus chain MB [auth M] Focus chain Q [auth H] Focus chain R [auth H] Focus chain RA [auth E] Focus chain Y [auth P] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain JA [auth C] Focus chain MB [auth M] Focus chain Q [auth H] Focus chain R [auth H] Focus chain RA [auth E] Focus chain Y [auth P]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain DB [auth K] SDF format, chain EB [auth K] SDF format, chain FA [auth B] SDF format, chain NA [auth D] SDF format, chain TB [auth N] SDF format, chain VA [auth F] SDF format, chain VB [auth O] SDF format, chain WB [auth O] SDF format, chain SA [auth E] MOL2 format, chain DB [auth K] MOL2 format, chain EB [auth K] MOL2 format, chain FA [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain TB [auth N] MOL2 format, chain VA [auth F] MOL2 format, chain VB [auth O] MOL2 format, chain WB [auth O] MOL2 format, chain SA [auth E] mmCIF format, chain DB [auth K] mmCIF format, chain EB [auth K] mmCIF format, chain FA [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain TB [auth N] mmCIF format, chain VA [auth F] mmCIF format, chain VB [auth O] mmCIF format, chain WB [auth O] mmCIF format, chain SA [auth E]	DB [auth K] EB [auth K] FA [auth B] NA [auth D] SA [auth E] DB [auth K], EB [auth K], FA [auth B], NA [auth D], SA [auth E], TB [auth N], VA [auth F], VB [auth O], WB [auth O]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DB [auth K] Focus chain EB [auth K] Focus chain FA [auth B] Focus chain NA [auth D] Focus chain SA [auth E] Focus chain TB [auth N] Focus chain VA [auth F] Focus chain VB [auth O] Focus chain WB [auth O] Interactions & Density Focus chain DB [auth K] Focus chain EB [auth K] Focus chain FA [auth B] Focus chain NA [auth D] Focus chain SA [auth E] Focus chain TB [auth N] Focus chain VA [auth F] Focus chain VB [auth O] Focus chain WB [auth O]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth J] SDF format, chain FB [auth K] SDF format, chain GA [auth B] SDF format, chain GB [auth K] SDF format, chain HA [auth B] SDF format, chain HB [auth K] SDF format, chain IB [auth K] SDF format, chain JB [auth K] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth D] SDF format, chain NB [auth M] SDF format, chain OA [auth D] SDF format, chain OB [auth M] SDF format, chain PA [auth D] SDF format, chain PB [auth M] SDF format, chain QB [auth M] SDF format, chain S [auth H] SDF format, chain T [auth H] SDF format, chain UA [auth F] SDF format, chain XA [auth G] SDF format, chain Z [auth P] SDF format, chain ZA [auth J] MOL2 format, chain AB [auth J] MOL2 format, chain FB [auth K] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth K] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth K] MOL2 format, chain IB [auth K] MOL2 format, chain JB [auth K] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain NB [auth M] MOL2 format, chain OA [auth D] MOL2 format, chain OB [auth M] MOL2 format, chain PA [auth D] MOL2 format, chain PB [auth M] MOL2 format, chain QB [auth M] MOL2 format, chain S [auth H] MOL2 format, chain T [auth H] MOL2 format, chain UA [auth F] MOL2 format, chain XA [auth G] MOL2 format, chain Z [auth P] MOL2 format, chain ZA [auth J] mmCIF format, chain AB [auth J] mmCIF format, chain FB [auth K] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth K] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth K] mmCIF format, chain IB [auth K] mmCIF format, chain JB [auth K] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain NB [auth M] mmCIF format, chain OA [auth D] mmCIF format, chain OB [auth M] mmCIF format, chain PA [auth D] mmCIF format, chain PB [auth M] mmCIF format, chain QB [auth M] mmCIF format, chain S [auth H] mmCIF format, chain T [auth H] mmCIF format, chain UA [auth F] mmCIF format, chain XA [auth G] mmCIF format, chain Z [auth P] mmCIF format, chain ZA [auth J]	AB [auth J] FB [auth K] GA [auth B] GB [auth K] HA [auth B] AB [auth J], FB [auth K], GA [auth B], GB [auth K], HA [auth B], HB [auth K], IB [auth K], JB [auth K], KA [auth C], LA [auth C], MA [auth D], NB [auth M], OA [auth D], OB [auth M], PA [auth D], PB [auth M], QB [auth M], S [auth H], T [auth H], UA [auth F], XA [auth G], Z [auth P], ZA [auth J]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth J] Focus chain FB [auth K] Focus chain GA [auth B] Focus chain GB [auth K] Focus chain HA [auth B] Focus chain HB [auth K] Focus chain IB [auth K] Focus chain JB [auth K] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth D] Focus chain NB [auth M] Focus chain OA [auth D] Focus chain OB [auth M] Focus chain PA [auth D] Focus chain PB [auth M] Focus chain QB [auth M] Focus chain S [auth H] Focus chain T [auth H] Focus chain UA [auth F] Focus chain XA [auth G] Focus chain Z [auth P] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth J] Focus chain FB [auth K] Focus chain GA [auth B] Focus chain GB [auth K] Focus chain HA [auth B] Focus chain HB [auth K] Focus chain IB [auth K] Focus chain JB [auth K] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth D] Focus chain NB [auth M] Focus chain OA [auth D] Focus chain OB [auth M] Focus chain PA [auth D] Focus chain PB [auth M] Focus chain QB [auth M] Focus chain S [auth H] Focus chain T [auth H] Focus chain UA [auth F] Focus chain XA [auth G] Focus chain Z [auth P] Focus chain ZA [auth J]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain CB [auth K] SDF format, chain IA [auth C] SDF format, chain KB [auth M] SDF format, chain P [auth H] SDF format, chain QA [auth E] SDF format, chain TA [auth F] SDF format, chain UB [auth O] SDF format, chain W [auth P] MOL2 format, chain AA [auth A] MOL2 format, chain CB [auth K] MOL2 format, chain IA [auth C] MOL2 format, chain KB [auth M] MOL2 format, chain P [auth H] MOL2 format, chain QA [auth E] MOL2 format, chain TA [auth F] MOL2 format, chain UB [auth O] MOL2 format, chain W [auth P] mmCIF format, chain AA [auth A] mmCIF format, chain CB [auth K] mmCIF format, chain IA [auth C] mmCIF format, chain KB [auth M] mmCIF format, chain P [auth H] mmCIF format, chain QA [auth E] mmCIF format, chain TA [auth F] mmCIF format, chain UB [auth O] mmCIF format, chain W [auth P]	AA [auth A] CB [auth K] IA [auth C] KB [auth M] P [auth H] AA [auth A], CB [auth K], IA [auth C], KB [auth M], P [auth H], QA [auth E], TA [auth F], UB [auth O], W [auth P]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain CB [auth K] Focus chain IA [auth C] Focus chain KB [auth M] Focus chain P [auth H] Focus chain QA [auth E] Focus chain TA [auth F] Focus chain UB [auth O] Focus chain W [auth P] Interactions & Density Focus chain AA [auth A] Focus chain CB [auth K] Focus chain IA [auth C] Focus chain KB [auth M] Focus chain P [auth H] Focus chain QA [auth E] Focus chain TA [auth F] Focus chain UB [auth O] Focus chain W [auth P]