8C5L

NR2F6 ligand binding domain in complex with NSD1 peptide

• PDB DOI: https://doi.org/10.2210/pdb8C5L/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli K-12, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-01-09 Released: 2024-01-10 
• Deposition Author(s): Oerlemans, G.J.M., van den Oetelaar, M.C.M., Brunsveld, L.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.233 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Structural insights into coregulator recruitment to the autorepressed NR2F6 nuclear receptor

Oerlemans, G.J.M., van den Oetelaar, M.C.M., Brunsveld, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 129.04 kDa 
• Atom Count: 8,752 
• Modelled Residue Count: 1,149 
• Deposited Residue Count: 1,174 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Nuclear receptor subfamily 2 group F member 6	A, B	568	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 8  Gene Names: malE, b4034, JW3994, NR2F6, EAR2, ERBAL2
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P10588 (Homo sapiens) Explore P10588  Go to UniProtKB:  P10588
PHAROS:  P10588 GTEx:  ENSG00000160113
UniProt Groups	P0AEX9P10588

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase, H3 lysine-36 specific	C, D	19	Homo sapiens	Mutation(s): 0  EC: 2.1.1.357
UniProt & NIH Common Fund Data Resources
Find proteins for Q96L73 (Homo sapiens) Explore Q96L73  Go to UniProtKB:  Q96L73
PHAROS:  Q96L73 GTEx:  ENSG00000165671

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	E [auth F], F [auth G]	2	N/A	N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	E [auth F], F [auth G]	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.233 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.383	α = 90
b = 170.383	β = 90
c = 83.667	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB-REDO	refinement
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Oerlemans, G.J.M., van den Oetelaar, M.C.M., Brunsveld, L.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	024.001.035

Revision History  

• Version 1.0: 2024-01-10
  Type: Initial release