Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 17.63 kDa 
• Atom Count: 1203 
• Residue Count: 129 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

6KCS

Crystal structure of HIRAN domain of HLTF in complex with duplex DNA

• DOI: 10.2210/pdb6KCS/pdb
• NDB: 6KCS

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-28 Released: 2020-06-10 
• Deposition Author(s): Hishiki, A., Hashimoto, A.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.264 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

Literature

Structure of HIRAN domain of human HLTF bound to duplex DNA provides structural basis for DNA unwinding to initiate replication fork regression.

Hishiki, A., Sato, M., Hashimoto, H.

(2020) J Biochem 167: 597-602

• PubMed: 31960921 
• DOI: 10.1093/jb/mvaa008
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Replication fork regression is a mechanism to rescue a stalled fork by various replication stresses, such as DNA lesions. Helicase-like transcription factor, a SNF2 translocase, plays a central role in the fork regression and its N-terminal domain, HIRAN (HIP116 and Rad5 N-terminal), binds the 3'-hydroxy group of single-stranded DNA. Furthermore, HIRAN is supposed to bind double-stranded DNA (dsDNA) and involved in strand separation in the fork regression, whereas structural basis for mechanisms underlying dsDNA binding and strand separation by HIRAN are still unclear. Here, we report the crystal structure of HIRAN bound to duplex DNA. The structure reveals that HIRAN binds the 3'-hydroxy group of DNA and unexpectedly unwinds three nucleobases of the duplex. Phe-142 is involved in the dsDNA binding and the strand separation. In addition, the structure unravels the mechanism underlying sequence-independent recognition for purine bases by HIRAN, where the N-glycosidic bond adopts syn conformation. Our findings indicate direct involvement of HIRAN in the fork regression by separating of the daughter strand from the parental template.

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Organizational Affiliation: 

School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8002, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Helicase-like transcription factor	A	122	Homo sapiens	Mutation(s): 0  Gene Names: HLTF, HIP116A, RNF80, SMARCA3, SNF2L3, ZBU1 EC: 2.3.2.27 (PDB Primary Data), 3.6.4 (PDB Primary Data)
Find proteins for Q14527 (Homo sapiens) Go to UniProtKB:  Q14527
NIH Common Fund Data Resources
PHAROS  Q14527 GTEx  ENSG00000071794

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*AP*CP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*GP*T)-3')	B	14	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.264 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.363	α = 90
b = 45.363	β = 90
c = 125.827	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-06-28 
• Released Date: 2020-06-10 
Deposition Author(s): Hishiki, A., Hashimoto, A.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	25291017
Japan Society for the Promotion of Science	Japan	16H04755
Japan Society for the Promotion of Science	Japan	23770125

Revision History 

• Version 1.0: 2020-06-10
  Type: Initial release