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- PDB-2xsz: The dodecameric human RuvBL1:RuvBL2 complex with truncated domains II -

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Basic information

Entry
Database: PDB / ID: 2xsz
TitleThe dodecameric human RuvBL1:RuvBL2 complex with truncated domains II
Components
  • RUVB-LIKE 1
  • RUVB-LIKE 2
KeywordsHYDROLASE / AAA+ PROTEINS / HELICASE / CHROMATIN REMODELLING
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 / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of DNA repair / DNA helicase activity / TBP-class protein binding / telomere maintenance / cellular response to estradiol stimulus / ADP binding / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / negative regulation of canonical Wnt signaling pathway / euchromatin / chromatin DNA binding / beta-catenin binding / nuclear matrix / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / UCH proteinases / cellular response to UV / nucleosome / unfolded protein binding / protein folding / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA helicase / DNA recombination / transcription coactivator activity / protein stabilization / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / cadherin binding / cell cycle / 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 / 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 / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities ...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 / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsGorynia, S. / Bandeiras, T.M. / Matias, P.M. / Pinho, F.G. / McVey, C.E. / Vonrhein, C. / Svergun, D.I. / Round, A. / Donner, P. / Carrondo, M.A.
Citation
Journal: J.Struct.Biol. / Year: 2011
Title: Structural and Functional Insights Into a Dodecameric Molecular Machine - the Ruvbl1/Ruvbl2 Complex.
Authors: Gorynia, S. / Bandeiras, T.M. / Pinho, F.G. / Mcvey, C.E. / Vonrhein, C. / Round, A. / Svergun, D.I. / Donner, P. / Matias, P.M. / Carrondo, M.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Cloning, Expression, Purification, Crystallization and Preliminary X-Ray Analysis of the Human Ruvbl1- Ruvbl2 Complex.
Authors: Gorynia, S. / Matias, P.M. / Bandeiras, T.M. / Donner, P. / Carrondo, M.A.
History
DepositionOct 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Aug 13, 2014Group: Refinement description
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUVB-LIKE 1
B: RUVB-LIKE 1
C: RUVB-LIKE 1
D: RUVB-LIKE 2
E: RUVB-LIKE 2
F: RUVB-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,30012
Polymers250,2576
Non-polymers3,0436
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27880 Å2
ΔGint-134.4 kcal/mol
Surface area77350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.824, 187.925, 244.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.39798, 0.83819, 0.37289), (-0.83583, -0.49884, 0.22923), (0.37815, -0.22045, 0.89911)11.6538, 110.91072, -3.16895
2given(-0.39865, -0.83952, 0.36917), (0.83265, -0.50005, -0.23799), (0.3844, 0.21251, 0.89837)98.86946, 45.42162, -26.17218
3given(-0.3927, 0.83843, 0.37792), (-0.83735, -0.49589, 0.23007), (0.38031, -0.2261, 0.8968)11.43878, 110.93247, -3.16107
4given(-0.40099, -0.84015, 0.36517), (0.83211, -0.50076, -0.23838), (0.38314, 0.20828, 0.8999)99.09162, 45.7303, -25.89621

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Components

#1: Protein RUVB-LIKE 1 / / RUVBL1 / 49 KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN / 49 KDA TBP-INTERACTING PROTEIN / ...RUVBL1 / 49 KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN / 49 KDA TBP-INTERACTING PROTEIN / TIP49A / PONTIN 52 / NUCLEAR MATRIX PROTEIN 238 / NMP 238 / 54 KDA ERYTHROCYTE CYTOSOLIC PROTEIN / ECP-54 / TIP60-ASSOCIATED PROTEIN 54-ALPHA / TAP54-ALPHA / INO80 COMPLEX SUBUNIT H


Mass: 40944.566 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: DOMAIN II WAS TRUNCATED BETWEEN RESIDUES T127 AND E233. A 4-RESIDUE LINKER WITH SEQUENCE GPPG WAS INSERTED TO REPLACE THE DELETED REGION
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETDUET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q9Y265, DNA helicase
#2: Protein RUVB-LIKE 2 / RUVBL2 / 48 KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN / 48 KDA TBP-INTERACTING PROTEIN / ...RUVBL2 / 48 KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN / 48 KDA TBP-INTERACTING PROTEIN / TIP49B / REPRESSING PONTIN 52 / REPTIN 52 / 51 KDA ERYTHROCYTE CYTOSOLIC PROTEIN / ECP-51 / TIP60-ASSOCIATED PROTEIN 54-BETA / TAP54-BETA / INO80 COMPLEX SUBUNIT J


Mass: 42474.375 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: DOMAIN II WAS TRUNCATED BETWEEN RESIDUES E134 AND E237. A 4-RESIDUE LINKER WITH SEQUENCE GPPG WAS INSERTED TO REPLACE THE DELETED REGION
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETDUET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q9Y230, DNA helicase
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Sequence detailsCHAINS A-C TRUNCATED BETWEEN RESIDUES T127 AND E233 CHAINS D-F TRUNCATED BETWEEN RESIDUES E134 AND ...CHAINS A-C TRUNCATED BETWEEN RESIDUES T127 AND E233 CHAINS D-F TRUNCATED BETWEEN RESIDUES E134 AND E237 IN EACH CASE A 4-RESIDUE LINKER WITH SEQUENCE GPPG WAS INSERTED.

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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: 53 %
Description: THE SE ATOM SUBSTRUCTURE WAS DETERMINED BY MOLECULAR REPLACEMENT.
Crystal growpH: 7.5
Details: CRYSTALLIZATION DROPS WERE MIXED FROM EQUAL VOLUMES OF PROTEIN SOLUTION (12 MG/ML, 20MM TRIS-HCL PH 8.0, 200MM NACL, 10% GLYCEROL, 4MM MGCL2, 4MM ADP, 0.5MM TCEP) AND CRYSTALLIZATION ...Details: CRYSTALLIZATION DROPS WERE MIXED FROM EQUAL VOLUMES OF PROTEIN SOLUTION (12 MG/ML, 20MM TRIS-HCL PH 8.0, 200MM NACL, 10% GLYCEROL, 4MM MGCL2, 4MM ADP, 0.5MM TCEP) AND CRYSTALLIZATION SOLUTION (0.2M MGCL2, 30% PEG 400, 0.1M HEPES PH 7.5).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97633
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 12, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
ReflectionResolution: 3→49 Å / Num. obs: 51774 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 99.32 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
autoSHARPphasing
BUSTER2.11.0refinement
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 2C9O

2c9o


Resolution: 3→46.14 Å / Cor.coef. Fo:Fc: 0.9462 / Cor.coef. Fo:Fc free: 0.9413 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.316
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 2632 5.1 %RANDOM
Rwork0.178 ---
obs0.1795 51736 99.6 %-
Displacement parametersBiso mean: 111.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.1724 Å20 Å20 Å2
2--15.7694 Å20 Å2
3----16.9418 Å2
Refine analyzeLuzzati coordinate error obs: 0.577 Å
Refinement stepCycle: LAST / Resolution: 3→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14478 0 186 0 14664
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00914839HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1420061HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5424SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes396HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2121HARMONIC5
X-RAY DIFFRACTIONt_it14839HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion20.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2075SEMIHARMONIC5
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_contact17190SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2702 219 5.76 %
Rwork0.2475 3580 -
all0.2489 3799 -
obs--99.6 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodOrigin x (Å)Origin y (Å)Origin z (Å)L11 (°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)
1refined61.895280.037720.0942
2refined13.000944.964140.60763.5764-0.0342-0.19112.5731-0.46291.2570.0286-0.10980.57660.1179-0.1016-0.0598-0.02430.02540.0729-0.341-0.0483-0.0013-0.28360.10480.1008
3refined14.689752.550232.29743.48590.58880.52833.02370.89652.2090.0564-0.8368-0.2890.8008-0.14830.72010.1659-0.18440.0919-0.1474-0.19150.3753-0.32860.01950.1309
4refined71.591923.924924.65843.052-0.4070.33244.3448-0.24871.29420.0696-0.33270.12230.3210.00860.82740.1975-0.248-0.0781-0.3149-0.10960.2714-0.3763-0.04710.1313
5refined61.09823.446419.18132.74-0.532-1.40353.54620.22482.79380.0102-0.5287-0.47010.8481-0.0399-0.5810.19970.44580.0297-0.1822-0.01640.0066-0.35160.23870.2263
6refined23.189478.977336.67522.88890.0915-1.00513.50130.42241.154-0.0002-0.0426-0.61930.262-0.21190.11180.14930.10360.2121-0.2317-0.00220.0547-0.40790.15360.1529
7refined31.365380.194527.05442.4051-1.50491.02344.1647-1.83612.3611-0.0487-0.58260.77280.8568-0.08840.3609-0.37950.00020.1371-0.2867-0.10180.332-0.424-0.2540.381
8refined37.123816.800932.91442.41220.1663-0.66972.2864-0.69411.35020.0762-0.23640.58270.3533-0.11690.1449-0.04550.03270.0407-0.267-0.040.1053-0.3813-0.1160.3279
9refined29.166225.860727.16173.71441.07350.75013.47151.40964.1744-0.0458-0.6313-0.83410.68-0.08870.16660.2691-0.12570.1346-0.239-0.07780.2935-0.41570.210.4036
10refined82.135859.981920.68112.4051-0.52460.0562.22720.29650.7854-0.0964-0.3035-0.44550.2793-0.07480.3430.1129-0.03010.1712-0.2006-0.14920.1689-0.41310.06250.1811
11refined76.11750.68514.66923.59910.2096-1.70981.67130.49314.3309-0.0945-0.7187-0.30160.1523-0.1349-0.4410.25420.68310.2294-0.33540.070.0448-0.08190.23310.1034
122.79360.383-0.24724.50610.22170.95050.0162-0.1486-0.4938-0.229-0.0949-0.39230.15330.23340.0787-0.37260.03590.0896-0.25680.2267-0.1201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 180:362)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 19:137 OR RESID 146:160 OR RESID 501)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 180:362)
4X-RAY DIFFRACTION4(CHAIN C AND RESID 19:139 OR RESID 145:159 OR RESID 501)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 180:364)
6X-RAY DIFFRACTION6D1
7X-RAY DIFFRACTION7(CHAIN D AND RESID 182:368)
8X-RAY DIFFRACTION8(CHAIN E AND RESID 37:146 OR RESID 155:168 OR RESID 501)
9X-RAY DIFFRACTION9(CHAIN E AND RESID 182:371)
10X-RAY DIFFRACTION10(CHAIN F AND RESID 37:146 OR RESID 155:168 OR RESID 501)
11X-RAY DIFFRACTION11(CHAIN F AND RESID 182:368)

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