9GI4 | pdb_00009gi4

TFIIIC5 DNA binding domain

• PDB DOI: https://doi.org/10.2210/pdb9GI4/pdb

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


• Deposited: 2024-08-16 Released: 2025-08-27 
• Deposition Author(s): Leen, E., Bayliss, R.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 
  0.300 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: in silico

Literature

N-myc interacts with TFIIIC via the DNA binding interface of TFIIIC5.

Leen, E., Bayliss, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 168.7 kDa 
• Atom Count: 9,306 
• Modeled Residue Count: 1,138 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor 3C polypeptide 5	A, B, C, D, E, F	242	Homo sapiens	Mutation(s): 0  Gene Names: GTF3C5, CDABP0017
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Q8 (Homo sapiens) Explore Q9Y5Q8  Go to UniProtKB:  Q9Y5Q8
PHAROS:  Q9Y5Q8 GTEx:  ENSG00000148308

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth B], I [auth C], J [auth D], K [auth D], L [auth E], M [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.300 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.524	α = 90.01
b = 37.644	β = 90.02
c = 276.677	γ = 59.9

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Leen, E., Bayliss, R.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/V029975/1

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release