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- PDB-5emx: Crystal structure of the S. cerevisiae Rtf1 histone modification ... -

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Basic information

Entry
Database: PDB / ID: 5emx
TitleCrystal structure of the S. cerevisiae Rtf1 histone modification domain mutant R124A R126A R128A
ComponentsRNA polymerase-associated protein RTF1
KeywordsTRANSCRIPTION / Paf1 / Chromatin / Rtf1
Function / homology
Function and homology information


snoRNA transcription by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / sno(s)RNA 3'-end processing / meiotic DNA double-strand break formation / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / global genome nucleotide-excision repair / mRNA 3'-end processing / : ...snoRNA transcription by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / sno(s)RNA 3'-end processing / meiotic DNA double-strand break formation / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / global genome nucleotide-excision repair / mRNA 3'-end processing / : / transcription elongation by RNA polymerase II / DNA-templated transcription termination / positive regulation of transcription elongation by RNA polymerase II / euchromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleus
Similarity search - Function
Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators.
Similarity search - Domain/homology
RNA polymerase-associated protein RTF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.399 Å
AuthorsWier, A.D. / Heroux, A. / VanDemark, A.P.
CitationJournal: Mol.Cell / Year: 2016
Title: The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6.
Authors: Van Oss, S.B. / Shirra, M.K. / Bataille, A.R. / Wier, A.D. / Yen, K. / Vinayachandran, V. / Byeon, I.L. / Cucinotta, C.E. / Heroux, A. / Jeon, J. / Kim, J. / VanDemark, A.P. / Pugh, B.F. / Arndt, K.M.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase-associated protein RTF1
B: RNA polymerase-associated protein RTF1


Theoretical massNumber of molelcules
Total (without water)17,0332
Polymers17,0332
Non-polymers00
Water1,40578
1
A: RNA polymerase-associated protein RTF1


Theoretical massNumber of molelcules
Total (without water)8,5161
Polymers8,5161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA polymerase-associated protein RTF1


Theoretical massNumber of molelcules
Total (without water)8,5161
Polymers8,5161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.271, 94.271, 76.842
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-232-

HOH

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Components

#1: Protein RNA polymerase-associated protein RTF1


Mass: 8516.430 Da / Num. of mol.: 2 / Fragment: UNP residues 74-139 / Mutation: R124A, R126A, R128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RTF1, CSL3, YGL244W, HRA458 / Production host: Escherichia coli (E. coli) / References: UniProt: P53064
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M phosphate-citrate (pH 4.2) and 40% PEG 300

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. obs: 30553 / % possible obs: 98.3 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 77.79
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.3 / % possible all: 78.5

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.399→14.626 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.178 998 3.85 %
Rwork0.1423 --
obs0.1436 25913 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→14.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 0 78 961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009943
X-RAY DIFFRACTIONf_angle_d1.0041268
X-RAY DIFFRACTIONf_dihedral_angle_d20.784382
X-RAY DIFFRACTIONf_chiral_restr0.066124
X-RAY DIFFRACTIONf_plane_restr0.006176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3991-1.47280.17631400.11563515X-RAY DIFFRACTION99
1.4728-1.5650.13931400.08543511X-RAY DIFFRACTION100
1.565-1.68570.13311420.08263535X-RAY DIFFRACTION100
1.6857-1.8550.11671430.09233548X-RAY DIFFRACTION100
1.855-2.12280.14191430.10523562X-RAY DIFFRACTION100
2.1228-2.67180.16151430.14613580X-RAY DIFFRACTION100
2.6718-14.62640.21421470.1743664X-RAY DIFFRACTION100

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