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- PDB-6k0r: Ruvbl1-Ruvbl2 with truncated domain II in complex with phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 6k0r
TitleRuvbl1-Ruvbl2 with truncated domain II in complex with phosphorylated Cordycepin
Components
  • RuvB-like 1,RuvB-like 1
  • RuvB-like 2,RuvB-like 2
KeywordsCIRCADIAN CLOCK PROTEIN / ATPase / Cordycepin
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 / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body / regulation of double-strand break repair ...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 / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body / regulation of double-strand break repair / Ino80 complex / box C/D snoRNP assembly / protein folding chaperone complex / NuA4 histone acetyltransferase complex / regulation of chromosome organization / regulation of DNA replication / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of double-strand break repair via homologous recombination / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / DNA helicase activity / TBP-class protein binding / telomere maintenance / positive regulation of DNA repair / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / ADP binding / DNA Damage Recognition in GG-NER / negative regulation of canonical Wnt signaling pathway / euchromatin / chromatin DNA binding / nuclear matrix / beta-catenin binding / transcription corepressor activity / cellular response to UV / UCH proteinases / unfolded protein binding / nucleosome / positive regulation of canonical Wnt signaling pathway / protein folding / HATs acetylate histones / ATPase binding / spermatogenesis / DNA helicase / regulation of apoptotic process / DNA recombination / transcription coactivator activity / regulation of cell cycle / protein stabilization / Ub-specific processing proteases / cadherin binding / chromatin remodeling / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / DNA repair / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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 / membrane / 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
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / ADENOSINE-5'-DIPHOSPHATE / Chem-CU0 / Chem-CUU / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsZhang, W. / Chen, L. / Li, W. / Ju, D. / Huang, N. / Zhang, E.
CitationJournal: Sci Transl Med / Year: 2020
Title: Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals.
Authors: Ju, D. / Zhang, W. / Yan, J. / Zhao, H. / Li, W. / Wang, J. / Liao, M. / Xu, Z. / Wang, Z. / Zhou, G. / Mei, L. / Hou, N. / Ying, S. / Cai, T. / Chen, S. / Xie, X. / Lai, L. / Tang, C. / ...Authors: Ju, D. / Zhang, W. / Yan, J. / Zhao, H. / Li, W. / Wang, J. / Liao, M. / Xu, Z. / Wang, Z. / Zhou, G. / Mei, L. / Hou, N. / Ying, S. / Cai, T. / Chen, S. / Xie, X. / Lai, L. / Tang, C. / Park, N. / Takahashi, J.S. / Huang, N. / Qi, X. / Zhang, E.E.
History
DepositionMay 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RuvB-like 1,RuvB-like 1
B: RuvB-like 1,RuvB-like 1
C: RuvB-like 1,RuvB-like 1
D: RuvB-like 2,RuvB-like 2
E: RuvB-like 2,RuvB-like 2
F: RuvB-like 2,RuvB-like 2
G: RuvB-like 1,RuvB-like 1
H: RuvB-like 1,RuvB-like 1
I: RuvB-like 1,RuvB-like 1
J: RuvB-like 2,RuvB-like 2
K: RuvB-like 2,RuvB-like 2
L: RuvB-like 2,RuvB-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,66626
Polymers474,62412
Non-polymers5,04214
Water1086
1
A: RuvB-like 1,RuvB-like 1
B: RuvB-like 1,RuvB-like 1
C: RuvB-like 1,RuvB-like 1
D: RuvB-like 2,RuvB-like 2
E: RuvB-like 2,RuvB-like 2
F: RuvB-like 2,RuvB-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,89913
Polymers237,3126
Non-polymers2,5877
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23500 Å2
ΔGint-144 kcal/mol
Surface area74280 Å2
MethodPISA
2
G: RuvB-like 1,RuvB-like 1
H: RuvB-like 1,RuvB-like 1
I: RuvB-like 1,RuvB-like 1
J: RuvB-like 2,RuvB-like 2
K: RuvB-like 2,RuvB-like 2
L: RuvB-like 2,RuvB-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,76613
Polymers237,3126
Non-polymers2,4547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21630 Å2
ΔGint-141 kcal/mol
Surface area73370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.304, 186.424, 235.176
Angle α, β, γ (deg.)90.000, 91.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 12 molecules ABCGHIDEFJKL

#1: Protein
RuvB-like 1,RuvB-like 1 / 49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa ...49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa erythrocyte cytosolic protein / ECP-54 / INO80 complex subunit H / Nuclear matrix protein 238 / NMP 238 / Pontin 52 / TIP49a / TIP60-associated protein 54-alpha / TAP54-alpha


Mass: 38840.000 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL1, INO80H, NMP238, TIP49, TIP49A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y265, DNA helicase
#2: Protein
RuvB-like 2,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: 40263.965 Da / Num. of mol.: 6
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

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Non-polymers , 6 types, 20 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CUU / [(2~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate


Mass: 411.202 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O9P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CU0 / [(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate


Mass: 294.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O10P2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES-Na pH 7.5-7.6, 0.2 M MgCl2, 20-21 % PEG400
PH range: 7.5-7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.502→235.137 Å / Num. obs: 90883 / % possible obs: 89.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 62.45 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.054 / Rrim(I) all: 0.12 / Net I/σ(I): 9.1
Reflection shellResolution: 2.502→2.81 Å / Rmerge(I) obs: 1.033 / Num. unique obs: 4542 / CC1/2: 0.159 / Rpim(I) all: 0.474 / Rrim(I) all: 1.138

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XSZ

2xsz


Resolution: 2.502→49.72 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.847 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.425
RfactorNum. reflection% reflectionSelection details
Rfree0.269 4436 4.88 %RANDOM
Rwork0.228 ---
obs0.23 90867 55.7 %-
Displacement parametersBiso max: 174.13 Å2 / Biso mean: 70.63 Å2 / Biso min: 26.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.9939 Å20 Å2-1.9771 Å2
2--9.0545 Å20 Å2
3----8.0606 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 2.502→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26860 0 314 6 27180
Biso mean--65.71 43.47 -
Num. residues----3705
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9262SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4645HARMONIC5
X-RAY DIFFRACTIONt_it27493HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion4032SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact31157SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d27493HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg37371HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion1.98
X-RAY DIFFRACTIONt_other_torsion21.59
LS refinement shellResolution: 2.502→2.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2316 104 5.72 %
Rwork0.2254 1714 -
all0.2257 1818 -
obs--6.06 %

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