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Open data
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Basic information
Entry | Database: PDB / ID: 6thl | ||||||
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Title | Crystal structure of the complex between RTT106 and BCD1 | ||||||
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![]() | CHAPERONE / SnoRNP | ||||||
Function / homology | ![]() sno(s)RNA metabolic process / snoRNA localization / transposition / pre-snoRNP complex / DNA replication-dependent chromatin assembly / box C/D snoRNP assembly / snoRNA binding / heterochromatin formation / nucleosome binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...sno(s)RNA metabolic process / snoRNA localization / transposition / pre-snoRNP complex / DNA replication-dependent chromatin assembly / box C/D snoRNP assembly / snoRNA binding / heterochromatin formation / nucleosome binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / transcription elongation by RNA polymerase II / ribosome biogenesis / chromatin organization / chromosome / histone binding / double-stranded DNA binding / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Charron, C. / Bragantini, B. / Manival, X. / Charpentier, B. | ||||||
![]() | ![]() Title: The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity. Authors: Bragantini, B. / Charron, C. / Bourguet, M. / Paul, A. / Tiotiu, D. / Rothe, B. / Marty, H. / Terral, G. / Hessmann, S. / Decourty, L. / Chagot, M.E. / Strub, J.M. / Massenet, S. / Bertrand, ...Authors: Bragantini, B. / Charron, C. / Bourguet, M. / Paul, A. / Tiotiu, D. / Rothe, B. / Marty, H. / Terral, G. / Hessmann, S. / Decourty, L. / Chagot, M.E. / Strub, J.M. / Massenet, S. / Bertrand, E. / Quinternet, M. / Saveanu, C. / Cianferani, S. / Labialle, S. / Manival, X. / Charpentier, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90 KB | Display | ![]() |
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PDB format | ![]() | 66 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.4 KB | Display | ![]() |
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Full document | ![]() | 440.1 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nz2SC ![]() 3tw1S 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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Unit cell |
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Components
#1: Protein | Mass: 27521.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RTT106, C1Q_03707 / Production host: ![]() ![]() |
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#2: Protein | Mass: 21571.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: BCD1, YHR040W / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Drops were made at 293 K by mixing the protein solution at 10 mg/mL and the reservoir solution containing 10 % (w/v) PEG 8K, 20 % (v/v) ethylene glycol, 10 mM 1,6-hexanediol, 10 mM 2- ...Details: Drops were made at 293 K by mixing the protein solution at 10 mg/mL and the reservoir solution containing 10 % (w/v) PEG 8K, 20 % (v/v) ethylene glycol, 10 mM 1,6-hexanediol, 10 mM 2-propanol and 100 mM sodium HEPES at pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. obs: 11730 / % possible obs: 99.1 % / Redundancy: 6.7 % / Rsym value: 0.047 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 2.79→2.95 Å / Num. unique obs: 1858 / Rsym value: 0.201 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TW1, 6NZ2 Resolution: 2.8→19.86 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.869 / SU B: 18.941 / SU ML: 0.369 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.476 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.18 Å2 / Biso mean: 58.036 Å2 / Biso min: 16.71 Å2
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Refinement step | Cycle: final / Resolution: 2.8→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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