8ZYS | pdb_00008zys

Crystal structure of HSF5 DNA-binding domain in complex with 3-site HSE DNA (25 bp)

• PDB DOI: https://doi.org/10.2210/pdb8ZYS/pdb
• NAKB: 8ZYS

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


• Deposited: 2024-06-18 Released: 2025-03-12 
• Deposition Author(s): Shi, X., Zhang, Q., Liu, W.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.241 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HSF5 DNA-binding domain in complex with 3-site HSE DNA (25 bp)

Shi, X., Zhang, Q., Liu, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 116.5 kDa 
• Atom Count: 7,166 
• Modeled Residue Count: 663 
• Deposited Residue Count: 874 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock factor protein 5	A, B, C, D, E, F	129	Homo sapiens	Mutation(s): 0  Gene Names: HSF5, HSTF5
UniProt & NIH Common Fund Data Resources
Find proteins for Q4G112 (Homo sapiens) Explore Q4G112  Go to UniProtKB:  Q4G112
PHAROS:  Q4G112 GTEx:  ENSG00000176160

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	G, I	25	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	H, J	25	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.241 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.96	α = 78.955
b = 50	β = 88.541
c = 126.88	γ = 73.066

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing
BUSTER	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Shi, X., Zhang, Q., Liu, W.

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Funding Organization	Location	Grant Number
Other government	China	2021XZL06
Other government	China	CSTB2022TIAD-STX0015
Other government	China	ZXZYTSYS02
Other government	China	23JSZ01

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-05-07
  Changes: Database references