7PA6 | pdb_00007pa6

JC polyomavirus VP1 in complex with scFv 27C11

PDB DOI: https://doi.org/10.2210/pdb7PA6/pdb

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens, JC polyomavirus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-07-29 Released: 2023-02-08
Deposition Author(s): Harprecht, C., Stroeh, L.J., Nagel, F., Freytag, J., Stehle, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.216 (Depositor), 0.222 (DCC)
R-Value Work:
0.183 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Structural characterization of human neutralizing antibodies against JC and BK polyomavirus

Harprecht, C., Stroeh, L.J., Senn, L., O'Hara, B.A., Nagel, F., Freytag, J., Stiehrof, Y.D., Atwood, W.J., Combaluzier, B., Stehle, T.

To be published.

Macromolecule Content

Total Structure Weight: 570.5 kDa
Atom Count: 40,319
Modeled Residue Count: 4,972
Deposited Residue Count: 5,250
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv 27C11 antibody heavy chain	A [auth KKK] B [auth LLL] C [auth MMM] D [auth NNN] E [auth OOO] A [auth KKK], B [auth LLL], C [auth MMM], D [auth NNN], E [auth OOO], F [auth PPP], G [auth QQQ], H [auth RRR], I [auth SSS], J [auth TTT]	253	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein VP1	K [auth AAA] L [auth BBB] M [auth CCC] N [auth DDD] O [auth EEE] K [auth AAA], L [auth BBB], M [auth CCC], N [auth DDD], O [auth EEE], P [auth FFF], Q [auth GGG], R [auth HHH], S [auth III], T [auth JJJ]	272	JC polyomavirus	Mutation(s): 0
UniProt
Find proteins for P03089 (JC polyomavirus) Explore P03089 Go to UniProtKB: P03089
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03089
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.216 (Depositor), 0.222 (DCC)
R-Value Work: 0.183 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.09	α = 100.913
b = 96.11	β = 93.012
c = 190.41	γ = 113.835

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-08

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FOR2327

Revision History (Full details and data files)

Version 1.0: 2023-02-08
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.