5EMC | pdb_00005emc

Transcription factor GRDBD and smGRE complex

• PDB DOI: https://doi.org/10.2210/pdb5EMC/pdb
• NAKB: 5EMC

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpHIS4
• Mutation(s): No 


• Deposited: 2015-11-06 Released: 2016-06-29 
• Deposition Author(s): Su, X.D., Lian, T., Jin, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.261 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

The effects of cytosine methylation on general transcription factors

Jin, J., Lian, T., SU, X.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 32.05 kDa 
• Atom Count: 1,973 
• Modeled Residue Count: 178 
• Deposited Residue Count: 224 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucocorticoid receptor	B [auth A], C [auth B]	94	Homo sapiens	Mutation(s): 0  Gene Names: NR3C1, GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens) Explore P04150  Go to UniProtKB:  P04150
PHAROS:  P04150 GTEx:  ENSG00000113580

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM)P*AP*TP*CP*AP*TP*GP*TP*TP*(5CM)P*TP*G)-3')	A [auth C]	18	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM)P*AP*TP*GP*AP*TP*GP*TP*TP*(5CM)P*TP*G)-3')	D	18	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.261 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.942	α = 90
b = 99.643	β = 90
c = 112.229	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data processing
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Su, X.D., Lian, T., Jin, J.

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations