8C1L | pdb_00008c1l

Crystal structure of HNF4 alpha LBD in complexes with palmitic acid and GRIP-1 peptide

• PDB DOI: https://doi.org/10.2210/pdb8C1L/pdb

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


• Deposited: 2022-12-20 Released: 2024-01-10 
• Deposition Author(s): Ni, X., Merk, D., Zhubi, R., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HNF4 alpha LBD in complexes with palmitic acid and GRIP-1 peptide

Ni, X., Merk, D., Zhubi, R., Knapp, S., Structural Genomics Consortium (SGC)

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.

Macromolecule Content 

• Total Structure Weight: 55.44 kDa 
• Atom Count: 3,647 
• Modeled Residue Count: 446 
• Deposited Residue Count: 482 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte nuclear factor 4-alpha	A, B	232	Homo sapiens	Mutation(s): 0  Gene Names: HNF4A, HNF4, NR2A1, TCF14
UniProt & NIH Common Fund Data Resources
Find proteins for P41235 (Homo sapiens) Explore P41235  Go to UniProtKB:  P41235
PHAROS:  P41235 GTEx:  ENSG00000101076

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	C [auth D], D [auth E]	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM (Subject of Investigation/LOI)	E [auth A], H [auth B]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.277	α = 90
b = 82.457	β = 111.84
c = 57.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Ni, X., Merk, D., Zhubi, R., Knapp, S., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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