7ZUO | pdb_00007zuo

Crystal Structure of Ljungan virus 4 2A2 protein, P212121 form

PDB DOI: https://doi.org/10.2210/pdb7ZUO/pdb

Classification: VIRAL PROTEIN
Organism(s): Ljungan virus 64-7855
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-12 Released: 2023-05-24
Deposition Author(s): von Castelmur, E., Perrakis, A.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.205 (Depositor), 0.214 (DCC)
R-Value Work:
0.172 (Depositor), 0.182 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7ZUO

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

Literature

Structural Plasticity of Parechovirus H/NC-motif 2A proteins

von Castelmur, E., Perrakis, A.

To be published.

Macromolecule Content

Total Structure Weight: 83.17 kDa
Atom Count: 6,148
Modeled Residue Count: 740
Deposited Residue Count: 750
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein 2A	A, B, C, D, E A, B, C, D, E, F	125	Ljungan virus 64-7855	Mutation(s): 0
UniProt
Find proteins for C0J6D4 (Ljungan virus 64-7855) Explore C0J6D4 Go to UniProtKB: C0J6D4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C0J6D4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain J [auth C] MOL2 format, chain M [auth F] MOL2 format, chain J [auth C] mmCIF format, chain M [auth F] mmCIF format, chain J [auth C]	J [auth C], M [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain M [auth F] Interactions & Density Focus chain J [auth C] Focus chain M [auth F]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain I [auth C] MOL2 format, chain L [auth D] MOL2 format, chain I [auth C] mmCIF format, chain L [auth D] mmCIF format, chain I [auth C]	I [auth C], L [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain I [auth C] Focus chain L [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.205 (Depositor), 0.214 (DCC)
R-Value Work: 0.172 (Depositor), 0.182 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.179	α = 90
b = 100.314	β = 90
c = 120.247	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-24

Deposition Author(s):

von Castelmur, E.

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	--

Revision History (Full details and data files)

Version 1.0: 2023-05-24
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description
Version 1.2: 2025-10-22
Changes: Data collection, 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.