4QYK | pdb_00004qyk

Crystal structure of a canine parvovirus variant

PDB DOI: https://doi.org/10.2210/pdb4QYK/pdb

Classification: VIRUS
Organism(s): Feline panleukopenia virus
Expression System: Felis catus
Mutation(s): No

Deposited: 2014-07-24 Released: 2014-12-10
Deposition Author(s): Lukk, T., Organtini, L.J., Hafenstein, S.U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.221 (Depositor), 0.222 (DCC)
R-Value Work:
0.180 (Depositor), 0.183 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Global Displacement of Canine Parvovirus by a Host-Adapted Variant: Structural Comparison between Pandemic Viruses with Distinct Host Ranges.

Organtini, L.J., Allison, A.B., Lukk, T., Parrish, C.R., Hafenstein, S.

(2015) J Virol 89: 1909-1912

PubMed: 25410876 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JVI.02611-14
Primary Citation of Related Structures:
4QYK

PubMed Abstract:
Canine parvovirus type 2 (CPV-2) emerged in 1978 and spread worldwide within 2 years. Subsequently, CPV-2 was completely replaced by the variant CPV-2a, which is characterized by four specific capsid (VP2) mutations. The X-ray crystal structure of the CPV-2a capsid shows that each mutation confers small local changes. The loss of a hydrogen bond and introduction of a glycine residue likely introduce flexibility to sites that control interactions with the host receptor, antibodies, and sialic acids.

Organizational Affiliation

Department of Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.

Macromolecule Content

Total Structure Weight: 1,943.1 kDa
Atom Count: 130,590
Modelled Residue Count: 16,440
Deposited Residue Count: 17,520
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A AA [auth a] B [auth E] BA [auth b] C [auth J] A, AA [auth a], B [auth E], BA [auth b], C [auth J], CA [auth c], D [auth N], DA [auth d], E [auth Q], F [auth B], G [auth C], H [auth D], I [auth F], J [auth G], K [auth H], L [auth I], M [auth K], N [auth L], O [auth M], P [auth O], Q [auth P], R, S, T, U, V, W, X, Y, Z	584	Feline panleukopenia virus	Mutation(s): 0
UniProt
Find proteins for P90456 (Feline panleukopenia virus) Explore P90456 Go to UniProtKB: P90456
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P90456
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BB [auth X] SDF format, chain EA [auth A] SDF format, chain HB [auth d] SDF format, chain KA [auth Q] SDF format, chain LA [auth B] SDF format, chain NA [auth D] SDF format, chain OA [auth G] SDF format, chain PA [auth H] SDF format, chain QA [auth H] SDF format, chain TA [auth L] SDF format, chain UA [auth M] SDF format, chain VA [auth O] SDF format, chain WA [auth P] SDF format, chain ZA [auth T] SDF format, chain AB [auth W] SDF format, chain CB [auth Y] SDF format, chain DB [auth Y] SDF format, chain EB [auth Z] SDF format, chain FA [auth E] SDF format, chain FB [auth c] SDF format, chain GA [auth E] SDF format, chain GB [auth d] SDF format, chain HA [auth J] SDF format, chain IA [auth J] SDF format, chain JA [auth N] SDF format, chain MA [auth C] SDF format, chain RA [auth I] SDF format, chain SA [auth K] SDF format, chain XA [auth R] SDF format, chain YA [auth S] MOL2 format, chain BB [auth X] MOL2 format, chain EA [auth A] MOL2 format, chain HB [auth d] MOL2 format, chain KA [auth Q] MOL2 format, chain LA [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth H] MOL2 format, chain QA [auth H] MOL2 format, chain TA [auth L] MOL2 format, chain UA [auth M] MOL2 format, chain VA [auth O] MOL2 format, chain WA [auth P] MOL2 format, chain ZA [auth T] MOL2 format, chain AB [auth W] MOL2 format, chain CB [auth Y] MOL2 format, chain DB [auth Y] MOL2 format, chain EB [auth Z] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth c] MOL2 format, chain GA [auth E] MOL2 format, chain GB [auth d] MOL2 format, chain HA [auth J] MOL2 format, chain IA [auth J] MOL2 format, chain JA [auth N] MOL2 format, chain MA [auth C] MOL2 format, chain RA [auth I] MOL2 format, chain SA [auth K] MOL2 format, chain XA [auth R] MOL2 format, chain YA [auth S] mmCIF format, chain BB [auth X] mmCIF format, chain EA [auth A] mmCIF format, chain HB [auth d] mmCIF format, chain KA [auth Q] mmCIF format, chain LA [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth G] mmCIF format, chain PA [auth H] mmCIF format, chain QA [auth H] mmCIF format, chain TA [auth L] mmCIF format, chain UA [auth M] mmCIF format, chain VA [auth O] mmCIF format, chain WA [auth P] mmCIF format, chain ZA [auth T] mmCIF format, chain AB [auth W] mmCIF format, chain CB [auth Y] mmCIF format, chain DB [auth Y] mmCIF format, chain EB [auth Z] mmCIF format, chain FA [auth E] mmCIF format, chain FB [auth c] mmCIF format, chain GA [auth E] mmCIF format, chain GB [auth d] mmCIF format, chain HA [auth J] mmCIF format, chain IA [auth J] mmCIF format, chain JA [auth N] mmCIF format, chain MA [auth C] mmCIF format, chain RA [auth I] mmCIF format, chain SA [auth K] mmCIF format, chain XA [auth R] mmCIF format, chain YA [auth S]	AB [auth W] BB [auth X] CB [auth Y] DB [auth Y] EA [auth A] AB [auth W], BB [auth X], CB [auth Y], DB [auth Y], EA [auth A], EB [auth Z], FA [auth E], FB [auth c], GA [auth E], GB [auth d], HA [auth J], HB [auth d], IA [auth J], JA [auth N], KA [auth Q], LA [auth B], MA [auth C], NA [auth D], OA [auth G], PA [auth H], QA [auth H], RA [auth I], SA [auth K], TA [auth L], UA [auth M], VA [auth O], WA [auth P], XA [auth R], YA [auth S], ZA [auth T]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth W] Focus chain BB [auth X] Focus chain CB [auth Y] Focus chain DB [auth Y] Focus chain EA [auth A] Focus chain EB [auth Z] Focus chain FA [auth E] Focus chain FB [auth c] Focus chain GA [auth E] Focus chain GB [auth d] Focus chain HA [auth J] Focus chain HB [auth d] Focus chain IA [auth J] Focus chain JA [auth N] Focus chain KA [auth Q] Focus chain LA [auth B] Focus chain MA [auth C] Focus chain NA [auth D] Focus chain OA [auth G] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain RA [auth I] Focus chain SA [auth K] Focus chain TA [auth L] Focus chain UA [auth M] Focus chain VA [auth O] Focus chain WA [auth P] Focus chain XA [auth R] Focus chain YA [auth S] Focus chain ZA [auth T] Interactions & Density Focus chain AB [auth W] Focus chain BB [auth X] Focus chain CB [auth Y] Focus chain DB [auth Y] Focus chain EA [auth A] Focus chain EB [auth Z] Focus chain FA [auth E] Focus chain FB [auth c] Focus chain GA [auth E] Focus chain GB [auth d] Focus chain HA [auth J] Focus chain HB [auth d] Focus chain IA [auth J] Focus chain JA [auth N] Focus chain KA [auth Q] Focus chain LA [auth B] Focus chain MA [auth C] Focus chain NA [auth D] Focus chain OA [auth G] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain RA [auth I] Focus chain SA [auth K] Focus chain TA [auth L] Focus chain UA [auth M] Focus chain VA [auth O] Focus chain WA [auth P] Focus chain XA [auth R] Focus chain YA [auth S] Focus chain ZA [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.221 (Depositor), 0.222 (DCC)
R-Value Work: 0.180 (Depositor), 0.183 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 453.1	α = 90
b = 453.1	β = 90
c = 319.02	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-12-10

Deposition Author(s):

Lukk, T.

Organtini, L.J.

Hafenstein, S.U.

Revision History (Full details and data files)

Version 1.0: 2014-12-10
Type: Initial release
Version 1.1: 2014-12-17
Changes: Advisory
Version 1.2: 2014-12-24
Changes: Structure summary
Version 1.3: 2015-01-28
Changes: Database references
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary