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

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
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This is version 1.1 of the entry. See complete history.

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.

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

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock factor protein 5	A, B, C, D, E 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4G112
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

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

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

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.