5JMM

Crystal structure of hERa-LBD (Y537S) in complex with biochanin A

• PDB DOI: https://doi.org/10.2210/pdb5JMM/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), synthetic construct
• Mutation(s): Yes 


• Deposited: 2016-04-29 Released: 2017-05-10 
• Deposition Author(s): Delfosse, V., Bourguet, W.
• Funding Organization(s): ANSES

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.216 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

Crystal structure of hERa-LBD (Y537S) in complex with biochanin A

Delfosse, V., Bourguet, V.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.12 kDa 
• Atom Count: 4,110 
• Modelled Residue Count: 485 
• Deposited Residue Count: 536 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A	255	Homo sapiens	Mutation(s): 1  Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	B	255	Homo sapiens	Mutation(s): 1  Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	C [auth F], D [auth G]	13	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1, BHLHE74, SRC1 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QSO	E [auth A], F [auth B]	5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one C16 H12 O5 WUADCCWRTIWANL-UHFFFAOYSA-N
GOL	G [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.216 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.4	α = 90
b = 81.22	β = 109.76
c = 58.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Delfosse, V., Bourguet, W.

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Funding Organization	Location	Grant Number
ANSES	France	EST-2013/1/031

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary