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- PDB-6h7x: First X-ray structure of full-length human RuvB-Like 2. -

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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 / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / Swr1 complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body ...promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / Swr1 complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / box C/D snoRNP assembly / protein folding chaperone complex / NuA4 histone acetyltransferase complex / regulation of chromosome organization / positive regulation of double-strand break repair via homologous recombination / regulation of DNA replication / MLL1 complex / TFIID-class transcription factor complex binding / regulation of embryonic development / Telomere Extension By Telomerase / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / positive regulation of DNA repair / TBP-class protein binding / DNA helicase activity / telomere maintenance / cellular response to estradiol stimulus / ADP binding / euchromatin / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / beta-catenin binding / nuclear matrix / transcription corepressor activity / cellular response to UV / unfolded protein binding / nucleosome / protein folding / HATs acetylate histones / ATPase binding / regulation of apoptotic process / DNA recombination / DNA helicase / protein stabilization / regulation of cell cycle / chromatin remodeling / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / ATP hydrolysis activity / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Ethylene glycol


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


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


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

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Experimental details

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Experiment

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

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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

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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

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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 )

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