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- PDB-5e8b: Crystal structure of the S. cerevisiae Rtf1 histone modification ... -

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Basic information

Entry
Database: PDB / ID: 5e8b
TitleCrystal structure of the S. cerevisiae Rtf1 histone modification domain mutant R126A
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 / global genome nucleotide-excision repair / Cdc73/Paf1 complex / 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 / global genome nucleotide-excision repair / Cdc73/Paf1 complex / mRNA 3'-end processing / : / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / DNA-templated transcription termination / 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
BENZAMIDINE / RNA polymerase-associated protein RTF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 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
DepositionOct 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4796
Polymers16,2902
Non-polymers1894
Water1,45981
1
A: RNA polymerase-associated protein RTF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1682
Polymers8,1451
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA polymerase-associated protein RTF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3114
Polymers8,1451
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.868, 93.868, 75.344
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
11B-325-

HOH

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Components

#1: Protein RNA polymerase-associated protein RTF1


Mass: 8145.050 Da / Num. of mol.: 2 / Fragment: UNP residues 74-139 / Mutation: R126A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RTF1, CSL3, YGL244W, HRA458 / Production host: Escherichia coli (E. coli) / References: UniProt: P53064
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M phosphate-citrate (pH 4.2), 28% PEG 300, Silver Bullets Bio condition 7 (Hampton)

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.62→28.451 Å / Num. obs: 16294 / % possible obs: 99.6 % / Redundancy: 20 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 43
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 15 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 6.77 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMX

5emx


Resolution: 1.62→28.451 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1926 816 5.01 %
Rwork0.1466 --
obs0.1489 16294 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→28.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 0 12 81 993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008925
X-RAY DIFFRACTIONf_angle_d0.8671231
X-RAY DIFFRACTIONf_dihedral_angle_d14.803584
X-RAY DIFFRACTIONf_chiral_restr0.039118
X-RAY DIFFRACTIONf_plane_restr0.005168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6201-1.72160.2261350.12972563X-RAY DIFFRACTION100
1.7216-1.85450.22061350.1342563X-RAY DIFFRACTION100
1.8545-2.0410.19981360.11782574X-RAY DIFFRACTION100
2.041-2.33620.18081350.11932561X-RAY DIFFRACTION100
2.3362-2.94290.21551360.14712600X-RAY DIFFRACTION100
2.9429-28.45510.17791390.16412617X-RAY DIFFRACTION98

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