[English] 日本語
Yorodumi
- PDB-1ixr: RuvA-RuvB complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ixr
TitleRuvA-RuvB complex
Components
  • Holliday junction DNA helicase ruvA
  • RuvB
KeywordsHYDROLASE / heterooligomeric complex / octameric RuvA / AAA-ATPase domain / complex with nucleotide
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA recombination / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Bacterial DNA recombination protein RuvA / DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB-like P-loop domain / Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvB, AAA lid domain / RuvA N terminal domain / RuvB C-terminal winged helix domain ...Bacterial DNA recombination protein RuvA / DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB-like P-loop domain / Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvB, AAA lid domain / RuvA N terminal domain / RuvB C-terminal winged helix domain / Holliday junction DNA helicase RuvB P-loop domain / RuvA, C-terminal domain / RuvB AAA lid domain / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helicase, Ruva Protein; domain 3 - #60 / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / 5' to 3' exonuclease, C-terminal subdomain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Holliday junction branch migration complex subunit RuvB / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsYamada, K. / Miyata, T. / Tsuchiya, D. / Oyama, T. / Fujiwara, Y. / Ohnishi, T. / Iwasaki, H. / Shinagawa, H. / Ariyoshi, M. / Mayanagi, K. / Morikawa, K.
CitationJournal: Mol.Cell / Year: 2002
Title: Crystal Structure of the RuvA-RuvB Complex: A Structural Basis for the Holliday Junction Migrating Motor Machinery
Authors: Yamada, K. / Miyata, T. / Tsuchiya, D. / Oyama, T. / Fujiwara, Y. / Ohnishi, T. / Iwasaki, H. / Shinagawa, H. / Ariyoshi, M. / Mayanagi, K. / Morikawa, K.
History
DepositionJul 4, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Holliday junction DNA helicase ruvA
B: Holliday junction DNA helicase ruvA
C: RuvB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1904
Polymers75,6833
Non-polymers5061
Water00
1
A: Holliday junction DNA helicase ruvA
B: Holliday junction DNA helicase ruvA
C: RuvB
hetero molecules

A: Holliday junction DNA helicase ruvA
B: Holliday junction DNA helicase ruvA
C: RuvB
hetero molecules

A: Holliday junction DNA helicase ruvA
B: Holliday junction DNA helicase ruvA
C: RuvB
hetero molecules

A: Holliday junction DNA helicase ruvA
B: Holliday junction DNA helicase ruvA
C: RuvB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,75816
Polymers302,73412
Non-polymers2,0254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)61.581, 195.113, 246.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is generated by the 222 crystallographic symmetry at the origin: (-x,-y,z), (x,-y,-z), and (-x,y,-z).

-
Components

#1: Protein Holliday junction DNA helicase ruvA


Mass: 20441.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ruvA / Plasmid: pTRA127 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9F1Q3
#2: Protein RuvB


Mass: 34801.312 Da / Num. of mol.: 1 / Fragment: residues 1-312 / Mutation: Y309R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ruvB / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SL87, EC: 3.6.1.3
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.88 Å3/Da / Density % sol: 74.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: NaCl, ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.6 mMRuvA1drop
20.8 mMRuvB1drop
31 mMAMPPNP1drop
410 mMTris-HCl1droppH8.0
50.1 M1dropNaCl
610 %(w/v)glycerol1drop
70.1 Msodium citrate1reservoirpH5.6
81.5 M1reservoirNaCl
90.1 M1reservoirMgCl2
1010 %(w/v)ethanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 24, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→44 Å / Num. all: 24710 / Num. obs: 24710 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 / Net I/σ(I): 28.9
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 3.5 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 44 Å / Num. measured all: 139789 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.474

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 3.3→12 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.335 965 -random
Rwork0.268 ---
all-20005 --
obs-20005 89.4 %-
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4873 0 31 0 4904
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.72
LS refinement shellResolution: 3.3→3.42 Å
RfactorNum. reflection% reflection
Rfree0.393 91 -
Rwork0.371 --
obs-1658 70.2 %
Refinement
*PLUS
Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.335 / Rfactor Rwork: 0.268
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.393 / Rfactor Rwork: 0.371

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more