8VQP | pdb_00008vqp

Crystal Structure Analysis of EGR1-MIDN

PDB DOI: https://doi.org/10.2210/pdb8VQP/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-18 Released: 2025-07-23
Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.271 (Depositor), 0.272 (DCC)
R-Value Work:
0.244 (Depositor), 0.244 (DCC)
R-Value Observed:
0.245 (Depositor)

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

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

Literature

Crystal Structure Analysis of EGR1-MIDN

Seo, H.-S., Dhe-Paganon, S.

To be published.

Macromolecule Content

Total Structure Weight: 16.54 kDa
Atom Count: 900
Modeled Residue Count: 119
Deposited Residue Count: 154
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EGR1-MIDN	A	154	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q504T8 (Homo sapiens) Explore Q504T8 Go to UniProtKB: Q504T8
PHAROS: Q504T8 GTEx: ENSG00000167470
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q504T8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.271 (Depositor), 0.272 (DCC)
R-Value Work: 0.244 (Depositor), 0.244 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.46	α = 90
b = 70.06	β = 90
c = 84.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

Dhe-Paganon, S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-07-23
Type: Initial release

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.