6L6Y | pdb_00006l6y

Crystal Structure of Pluripotency Reprogramming Factor Sox17 mutant (Sox17EK) HMG Domain bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb6L6Y/pdb
• NAKB: 6L6Y

• Classification: DNA BINDING PROTEIN/DNA,TRANSCRIPTION
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-10-29 Released: 2020-11-04 
• Deposition Author(s): Balasubramanian, M., Kolatkar, P.R.
• Funding Organization(s): Qatar Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Pluripotency Reprogramming Factor Sox17 mutant (Sox17EK) HMG Domain bound to DNA

Balasubramanian, M., Kolatkar, P.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.86 kDa 
• Atom Count: 2,680 
• Modeled Residue Count: 224 
• Deposited Residue Count: 230 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor SOX-17	C [auth D], F	83	Mus musculus	Mutation(s): 1  Gene Names: Sox17, Sox-17
UniProt
Find proteins for Q61473 (Mus musculus) Explore Q61473  Go to UniProtKB:  Q61473

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)-3')	A, D [auth C]	16	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')	B, E	16	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	G [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.04	α = 90
b = 73.205	β = 90
c = 81.952	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PROTEUM	data reduction
SADABS	data scaling
PHENIX	phasing
PROTEUM	data collection

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Balasubramanian, M., Kolatkar, P.R.

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Funding Organization	Location	Grant Number
Qatar Foundation	Qatar	IGP1 2014-004

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description