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- PDB-2xsz: The dodecameric human RuvBL1:RuvBL2 complex with truncated domains II -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xsz | ||||||
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Title | The dodecameric human RuvBL1:RuvBL2 complex with truncated domains II | ||||||
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![]() | HYDROLASE / AAA+ PROTEINS / HELICASE / CHROMATIN REMODELLING | ||||||
Function / homology | ![]() 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 / Telomere Extension By Telomerase / protein folding chaperone complex / box C/D snoRNP assembly / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of DNA replication / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / positive regulation of double-strand break repair via homologous recombination / positive regulation of DNA repair / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / cellular response to estradiol stimulus / TBP-class protein binding / DNA helicase activity / telomere maintenance / 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 / ADP binding / nuclear matrix / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / UCH proteinases / cellular response to UV / nucleosome / unfolded protein binding / protein folding / ATPase binding / HATs acetylate histones / spermatogenesis / DNA helicase / DNA recombination / regulation of apoptotic process / transcription coactivator activity / chromatin remodeling / protein stabilization / regulation of cell cycle / Ub-specific processing proteases / cadherin binding / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / DNA repair / centrosome / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gorynia, 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. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 759.2 KB | Display | ![]() |
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PDB format | ![]() | 634.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2c9oS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | 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.) ![]() ![]() ![]() #2: Protein | 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.) ![]() ![]() ![]() #3: Chemical | ChemComp-ATP / Sequence details | CHAINS 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
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % Description: THE SE ATOM SUBSTRUCTURE WAS DETERMINED BY MOLECULAR REPLACEMENT. |
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Crystal grow | pH: 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). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 12, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97633 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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
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Displacement parameters | Biso mean: 111.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.577 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→46.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 Å / Total num. of bins used: 20
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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