[English] 日本語
Yorodumi
- PDB-6h7x: First X-ray structure of full-length human RuvB-Like 2. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h7x
TitleFirst X-ray structure of full-length human RuvB-Like 2.
ComponentsRuvB-like 2
KeywordsCHAPERONE / ATPase / helicase
Function / homology
Function and homology information


promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / Ino80 complex ...promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / Ino80 complex / regulation of double-strand break repair / box C/D snoRNP assembly / protein folding chaperone complex / NuA4 histone acetyltransferase complex / regulation of chromosome organization / TFIID-class transcription factor complex binding / regulation of DNA replication / MLL1 complex / regulation of embryonic development / Telomere Extension By Telomerase / positive regulation of double-strand break repair via homologous recombination / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / telomere maintenance / DNA helicase activity / positive regulation of DNA repair / TBP-class protein binding / cellular response to estradiol stimulus / chromatin DNA binding / euchromatin / negative regulation of canonical Wnt signaling pathway / ADP binding / beta-catenin binding / nuclear matrix / cellular response to UV / transcription corepressor activity / unfolded protein binding / nucleosome / protein folding / HATs acetylate histones / ATPase binding / regulation of apoptotic process / DNA recombination / DNA helicase / regulation of cell cycle / protein stabilization / ciliary basal body / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ribonucleoprotein complex / DNA repair / centrosome / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RuvB-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.892 Å
AuthorsSilva, S. / Brito, J.A. / Matias, P. / Bandeiras, T.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Other governmentSFRH/BD/78706/2011/ Portugal
CitationJournal: Sci Rep / Year: 2018
Title: X-ray structure of full-length human RuvB-Like 2 - mechanistic insights into coupling between ATP binding and mechanical action.
Authors: Silva, S.T.N. / Brito, J.A. / Arranz, R. / Sorzano, C.O.S. / Ebel, C. / Doutch, J. / Tully, M.D. / Carazo, J.M. / Carrascosa, J.L. / Matias, P.M. / Bandeiras, T.M.
History
DepositionJul 31, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionAug 8, 2018ID: 5N7R
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RuvB-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,83612
Polymers51,2221
Non-polymers61411
Water72140
1
A: RuvB-like 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)311,01672
Polymers307,3356
Non-polymers3,68166
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Buried area40950 Å2
ΔGint-174 kcal/mol
Surface area106600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.023, 123.023, 60.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein RuvB-like 2 / 48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa ...48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa erythrocyte cytosolic protein / ECP-51 / INO80 complex subunit J / Repressing pontin 52 / Reptin 52 / TIP49b / TIP60-associated protein 54-beta / TAP54-beta


Mass: 51222.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y230, DNA helicase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.63 % / Description: Hexagonal needle
Crystal growTemperature: 303.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 3350, Magnesium Chloride

-
Data collection

DiffractionMean temperature: 273.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.892→52.859 Å / Num. obs: 11583 / % possible obs: 97 % / Redundancy: 3.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.063 / Rrim(I) all: 0.129 / Net I/σ(I): 11.3
Reflection shellResolution: 2.892→2.94 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2992: ???)refinement
autoPROCdata collection
BUCCANEERmodel building
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c9o

2c9o


Resolution: 2.892→40.269 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.45
RfactorNum. reflection% reflection
Rfree0.2373 534 4.61 %
Rwork0.205 --
obs0.2065 11578 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.892→40.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 38 40 2962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022940
X-RAY DIFFRACTIONf_angle_d0.4243936
X-RAY DIFFRACTIONf_dihedral_angle_d11.8241812
X-RAY DIFFRACTIONf_chiral_restr0.041467
X-RAY DIFFRACTIONf_plane_restr0.002498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8916-3.18250.31181390.26752761X-RAY DIFFRACTION98
3.1825-3.64270.2381500.20882727X-RAY DIFFRACTION97
3.6427-4.58840.20221210.18062772X-RAY DIFFRACTION97
4.5884-40.27260.23661240.20222784X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.68250.57530.13631.224-0.09121.61990.0042-0.48520.05380.1150.0555-0.21070.12750.3592-0.03220.29010.0479-0.06180.41060.00490.359298.2562105.8235-21.7917
24.254-2.15083.3130.6657-1.51712.08970.48410.7137-0.5941-0.1445-0.2690.10230.01720.4728-0.21010.5155-0-0.17870.79010.0060.6392119.510692.92374.3736
32.6972-0.26081.51.863-0.55593.93610.0054-0.2826-0.01670.08630.0634-0.09940.2108-0.0833-0.07030.2863-0.00110.00360.3005-0.06510.249586.8781108.625-18.1982
40.71021.5040.29784.11230.18380.597-0.12050.2753-0.1853-0.14650.2419-0.66970.11280.1557-0.0920.33380.04940.05430.4162-0.07060.355194.913984.3749-41.1898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 251 )
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 347 )
4X-RAY DIFFRACTION4chain 'A' and (resid 348 through 456 )

+
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