9ZRC | pdb_00009zrc

Crystal structure of macrodomain from Eastern Equine Encephalitis Virus i

PDB DOI: https://doi.org/10.2210/pdb9ZRC/pdb

Classification: VIRAL PROTEIN
Organism(s): Eastern equine encephalitis virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-12-19 Released: 2026-08-12
Deposition Author(s): Chang, C., Endre, M., Stols, L., Kim, Y., Joachimiak, A.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.173 (Depositor), 0.172 (DCC)
R-Value Work:
0.145 (Depositor), 0.144 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of macrodomain from Chikungunya virus

Chang, C., Endre, M., Stols, L., Kim, Y., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 17.55 kDa
Atom Count: 1,530
Modeled Residue Count: 156
Deposited Residue Count: 158
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein P1234	A	158	Eastern equine encephalitis virus	Mutation(s): 0
UniProt
Find proteins for Q66580 (Eastern equine encephalitis virus) Explore Q66580 Go to UniProtKB: Q66580
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q66580
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.173 (Depositor), 0.172 (DCC)
R-Value Work: 0.145 (Depositor), 0.144 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.45	α = 90
b = 47.727	β = 90
c = 66.906	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-08-12
Type: Initial release

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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.