1HQC | pdb_00001hqc

STRUCTURE OF RUVB FROM THERMUS THERMOPHILUS HB8

• PDB DOI: https://doi.org/10.2210/pdb1HQC/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2000-12-15 Released: 2001-02-21 
• Deposition Author(s): Yamada, K., Kunishima, N., Mayanagi, K., Iwasaki, H., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.296 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.260 (DCC) 

Literature

Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8.

Yamada, K., Kunishima, N., Mayanagi, K., Ohnishi, T., Nishino, T., Iwasaki, H., Shinagawa, H., Morikawa, K.

(2001) Proc Natl Acad Sci U S A 98: 1442-1447

• PubMed: 11171970 
• DOI: https://doi.org/10.1073/pnas.98.4.1442
• Primary Citation Related Structures: 
  1HQC


• PubMed Abstract: 
  

  We report here the crystal structure of the RuvB motor protein from Thermus thermophilus HB8, which drives branch migration of the Holliday junction during homologous recombination. RuvB has a crescent-like architecture consisting of three consecutive domains, the first two of which are involved in ATP binding and hydrolysis. DNA is likely to interact with a large basic cleft, which encompasses the ATP-binding pocket and domain boundaries, whereas the junction-recognition protein RuvA may bind a flexible beta-hairpin protruding from the N-terminal domain. The structures of two subunits, related by a noncrystallographic pseudo-2-fold axis, imply that conformational changes of motor protein coupled with ATP hydrolysis may reflect motility essential for its translocation around double-stranded DNA.

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Organizational Affiliation: 
• Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.

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.

Macromolecule Content 

• Total Structure Weight: 72.42 kDa 
• Atom Count: 4,944 
• Modeled Residue Count: 628 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RUVB	A, B	324	Thermus thermophilus	Mutation(s): 0  Gene Names: RUVB EC: 3.6.1.3 (PDB Primary Data), 3.6.4 (UniProt)
UniProt
Find proteins for Q5SL87 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SL87  Go to UniProtKB:  Q5SL87

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	D [auth A], F [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.296 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.260 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.865	α = 90
b = 84.865	β = 90
c = 355.24	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-21 
Deposition Author(s): Yamada, K., Kunishima, N., Mayanagi, K., Iwasaki, H., Morikawa, K.

Revision History  

• Version 1.0: 2001-02-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations