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- PDB-6thl: Crystal structure of the complex between RTT106 and BCD1 -

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Basic information

Entry
Database: PDB / ID: 6thl
TitleCrystal structure of the complex between RTT106 and BCD1
Components
  • Box C/D snoRNA protein 1
  • Rtt106p
KeywordsCHAPERONE / SnoRNP
Function / homology
Function and homology information


sno(s)RNA metabolic process / snoRNA localization / transposition / pre-snoRNP complex / DNA replication-dependent chromatin assembly / box C/D snoRNP assembly / snoRNA binding / nucleosome binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / transcription elongation by RNA polymerase II ...sno(s)RNA metabolic process / snoRNA localization / transposition / pre-snoRNP complex / DNA replication-dependent chromatin assembly / box C/D snoRNP assembly / snoRNA binding / nucleosome binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / transcription elongation by RNA polymerase II / heterochromatin formation / ribosome biogenesis / chromatin organization / chromosome / histone binding / double-stranded DNA binding / negative regulation of transcription by RNA polymerase II / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / Rtt106, pleckstrin homology domain / Histone chaperone Rtt106, N-terminal domain / Histone chaperone Rtt106, N-terminal domain superfamily / Histone chaperone Rtt106 N-terminal domain / Pleckstrin homology domain / HIT zinc finger / Zinc finger HIT-type profile. / : / Zinc finger, HIT-type ...: / Rtt106, pleckstrin homology domain / Histone chaperone Rtt106, N-terminal domain / Histone chaperone Rtt106, N-terminal domain superfamily / Histone chaperone Rtt106 N-terminal domain / Pleckstrin homology domain / HIT zinc finger / Zinc finger HIT-type profile. / : / Zinc finger, HIT-type / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / PH-like domain superfamily
Similarity search - Domain/homology
Histone chaperone RTT106 / Box C/D snoRNA protein 1 / Histone chaperone RTT106
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsCharron, C. / Bragantini, B. / Manival, X. / Charpentier, B.
CitationJournal: Nat Commun / Year: 2021
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
DepositionNov 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rtt106p
B: Box C/D snoRNA protein 1


Theoretical massNumber of molelcules
Total (without water)49,0942
Polymers49,0942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-4 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.712, 66.684, 65.122
Angle α, β, γ (deg.)90.000, 104.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rtt106p


Mass: 27521.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RTT106, C1Q_03707 / Production host: Escherichia coli (E. coli) / References: UniProt: C7GTH4, UniProt: P40161*PLUS
#2: Protein Box C/D snoRNA protein 1


Mass: 21571.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BCD1, YHR040W / Production host: Escherichia coli (E. coli) / References: UniProt: P38772

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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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.79→2.95 Å / Num. unique obs: 1858 / Rsym value: 0.201

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
XDSdata reduction
XPREPdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW1, 6NZ2

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2997 1135 10 %RANDOM
Rwork0.21 ---
obs0.2191 10224 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.18 Å2 / Biso mean: 58.036 Å2 / Biso min: 16.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å20.07 Å2
2---0.05 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.8→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 0 0 3007
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193065
X-RAY DIFFRACTIONr_bond_other_d0.0010.022986
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9724123
X-RAY DIFFRACTIONr_angle_other_deg0.8236904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1265362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28224.745137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44615590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0671512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02677
LS refinement shellResolution: 2.8→2.871 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 83 -
Rwork0.372 727 -
all-810 -
obs--97.47 %

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