8IFO

Crystal structure of estrogen related receptor-gamma DNA binding domain complexed with Pla2g12b promoter

PDB DOI: https://doi.org/10.2210/pdb8IFO/pdb
NAKB: 8IFO

Classification: TRANSCRIPTION
Organism(s): Homo sapiens, Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-19 Released: 2023-03-29
Deposition Author(s): Xu, T., Zhen, X., Liu, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.260
R-Value Work: 0.219
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

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

Literature

ERR gamma-DBD undergoes dimerization and conformational rearrangement upon binding to the downstream site of the DR1 element

Zhen, X., Gan, Q., Qu, L., Dong, Y., Pan, C., Liu, J., Wang, N., Xu, T.

(2023) Biochem Biophys Res Commun 656: 16-22

DOI: https://doi.org/10.1016/j.bbrc.2023.03.038

Macromolecule Content

Total Structure Weight: 58.14 kDa
Atom Count: 3,310
Modelled Residue Count: 301
Deposited Residue Count: 383
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen-related receptor gamma	A, B, E [auth F]	105	Homo sapiens	Mutation(s): 0 Gene Names: ESRRG, ERR3, ERRG2, KIAA0832, NR3B3
UniProt & NIH Common Fund Data Resources
Find proteins for P62508 (Homo sapiens) Explore P62508 Go to UniProtKB: P62508
PHAROS: P62508 GTEx: ENSG00000196482
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62508
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPAPGPGPAPCPAPAPAPGPGPTPGPAPAPAP*C)-3')	C, F [auth G]	17	Mus musculus
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPTPTPTPCPAPCPCPTPTPTPGPTPCPCPTP*C)-3')	D, G [auth H]	17	Mus musculus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth F] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth F]	M [auth B], N [auth C], Q [auth F]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Focus chain N [auth C] Focus chain Q [auth F] Interactions & Density Focus chain M [auth B] Focus chain N [auth C] Focus chain Q [auth F]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth F] SDF format, chain P [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F]	H [auth A] I [auth A] J [auth A] K [auth B] L [auth B] H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], O [auth F], P [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth F] Focus chain P [auth F]