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Open data
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Basic information
Entry | Database: PDB / ID: 5fm7 | ||||||
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Title | Double-heterohexameric rings of full-length Rvb1(ADP)Rvb2(ADP) | ||||||
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![]() | ATP BINDING PROTEIN | ||||||
Function / homology | ![]() R2TP complex / Swr1 complex / Ino80 complex / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex / DNA helicase activity / DNA helicase / chromatin remodeling / DNA repair / regulation of transcription by RNA polymerase II ...R2TP complex / Swr1 complex / Ino80 complex / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex / DNA helicase activity / DNA helicase / chromatin remodeling / DNA repair / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Silva-Martin, N. / Dauden, M.I. / Glatt, S. / Hoffmann, N.A. / Mueller, C.W. | ||||||
![]() | ![]() Title: The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex. Authors: Noella Silva-Martin / María I Daudén / Sebastian Glatt / Niklas A Hoffmann / Panagiotis Kastritis / Peer Bork / Martin Beck / Christoph W Müller / ![]() Abstract: The Rvb1/Rvb2 complex is an essential component of many cellular pathways. The Rvb1/Rvb2 complex forms a dodecameric assembly where six copies of each subunit form two heterohexameric rings. However, ...The Rvb1/Rvb2 complex is an essential component of many cellular pathways. The Rvb1/Rvb2 complex forms a dodecameric assembly where six copies of each subunit form two heterohexameric rings. However, due to conformational variability, the way the two rings pack together is still not fully understood. Here, we present the crystal structure and two cryo-electron microscopy reconstructions of the dodecameric, full-length Rvb1/Rvb2 complex, all showing that the interaction between the two heterohexameric rings is mediated through the Rvb1/Rvb2-specific domain II. Two conformations of the Rvb1/Rvb2 dodecamer are present in solution: a stretched conformation also present in the crystal, and a compact conformation. Novel asymmetric features observed in the reconstruction of the compact conformation provide additional insight into the plasticity of the Rvb1/Rvb2 complex. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343.7 KB | Display | ![]() |
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PDB format | ![]() | 282.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3242C ![]() 3243C ![]() 5fm6SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50579.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 53340.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | Sequence details | N-TERMINAL GA STEMS FROM TEV CLEAVAGE SITE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.97 % / Description: NONE |
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Crystal grow | Details: 0.1 M MES PH 6.0,1 M SUCCINATE, 1.2% MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 25695 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 118.85 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.8 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5FM6 Resolution: 2.901→48.632 Å / SU ML: 0.6 / σ(F): 1.34 / Phase error: 34.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.901→48.632 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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