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- PDB-5zyp: Structure of the Yeast Ctr9/Paf1 complex -

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Basic information

Entry
Database: PDB / ID: 5zyp
TitleStructure of the Yeast Ctr9/Paf1 complex
ComponentsRNA polymerase-associated protein CTR9,RNA polymerase II-associated protein 1
KeywordsTRANSCRIPTION / Transciption / Complex / TPR
Function / homology
Function and homology information


snoRNA transcription by RNA polymerase II / sno(s)RNA transcription / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription initiation by RNA polymerase II / sno(s)RNA 3'-end processing / regulation of transcription-coupled nucleotide-excision repair / RNA polymerase II C-terminal domain phosphoserine binding / triplex DNA binding / Cdc73/Paf1 complex / global genome nucleotide-excision repair ...snoRNA transcription by RNA polymerase II / sno(s)RNA transcription / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription initiation by RNA polymerase II / sno(s)RNA 3'-end processing / regulation of transcription-coupled nucleotide-excision repair / RNA polymerase II C-terminal domain phosphoserine binding / triplex DNA binding / Cdc73/Paf1 complex / global genome nucleotide-excision repair / negative regulation of DNA recombination / rDNA heterochromatin formation / mRNA 3'-end processing / negative regulation of mitophagy / RNA polymerase II complex binding / transcription by RNA polymerase III / transcription elongation by RNA polymerase I / transcription by RNA polymerase I / transcription coregulator activity / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / DNA-templated transcription termination / euchromatin / rRNA processing / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
RNA polymerase II associated factor Paf1 / Paf1 / RNA polymerase-associated protein Ctr9 / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / RNA polymerase II-associated protein 1 / RNA polymerase-associated protein CTR9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.532 Å
AuthorsXie, Y. / Zheng, M. / Zhou, H. / Long, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2014CB910201 China
National Natural Science Foundation of China31470755 China
National Natural Science Foundation of China31670758 China
CitationJournal: Nat Commun / Year: 2018
Title: Paf1 and Ctr9 subcomplex formation is essential for Paf1 complex assembly and functional regulation.
Authors: Xie, Y. / Zheng, M. / Chu, X. / Chen, Y. / Xu, H. / Wang, J. / Zhou, H. / Long, J.
History
DepositionMay 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / 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 1.2Nov 13, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature / 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_audit_support.funding_organization / _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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase-associated protein CTR9,RNA polymerase II-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2794
Polymers45,1031
Non-polymers1763
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.953, 95.953, 115.498
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-802-

NI

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Components

#1: Protein RNA polymerase-associated protein CTR9,RNA polymerase II-associated protein 1 / Centromere-binding factor 1-dependent protein 1 / Cln three-requiring protein 9 / Protein PAF1


Mass: 45102.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fusion protein of residues 1-313 from CTR9 (UNP P89105) and residues from 34-103 from Paf1 (RNA polymerase II-associated protein 1, UNP P38351)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CTR9, CDP1, YOL145C, PAF1, YBR279W, YBR2016 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P89105, UniProt: P38351
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl, pH8.5, 0.8M Lithium sulfate, 0.01M Nickel chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 35677 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rpim(I) all: 0.022 / Net I/σ(I): 29.2
Reflection shellResolution: 2.53→2.62 Å / Num. unique obs: 2051 / Rpim(I) all: 0.395

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155_000)refinement
HKL-2000v714data reduction
HKL-2000v714data scaling
PHENIX(1.10_2155_000)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.532→47.976 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.02
RfactorNum. reflection% reflection
Rfree0.243 3579 10.03 %
Rwork0.1938 --
obs0.1989 35677 90.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.532→47.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 3 85 2827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082791
X-RAY DIFFRACTIONf_angle_d0.9843780
X-RAY DIFFRACTIONf_dihedral_angle_d18.8571699
X-RAY DIFFRACTIONf_chiral_restr0.049436
X-RAY DIFFRACTIONf_plane_restr0.006478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5322-2.56550.3374400.2463355X-RAY DIFFRACTION26
2.5655-2.60060.2544680.2473560X-RAY DIFFRACTION41
2.6006-2.63780.3219840.2295828X-RAY DIFFRACTION61
2.6378-2.67720.30241090.228958X-RAY DIFFRACTION70
2.6772-2.7190.23611160.23861044X-RAY DIFFRACTION77
2.719-2.76360.27181360.22721230X-RAY DIFFRACTION88
2.7636-2.81120.29931410.2221293X-RAY DIFFRACTION95
2.8112-2.86230.30261490.231292X-RAY DIFFRACTION96
2.8623-2.91740.27441410.22171379X-RAY DIFFRACTION100
2.9174-2.97690.2981550.23751368X-RAY DIFFRACTION100
2.9769-3.04160.24651540.22591350X-RAY DIFFRACTION100
3.0416-3.11240.32061580.23411386X-RAY DIFFRACTION99
3.1124-3.19020.26641530.21371353X-RAY DIFFRACTION99
3.1902-3.27640.2741620.22691350X-RAY DIFFRACTION99
3.2764-3.37280.23851460.21481345X-RAY DIFFRACTION99
3.3728-3.48170.24761520.20241386X-RAY DIFFRACTION99
3.4817-3.60610.26971450.19561387X-RAY DIFFRACTION100
3.6061-3.75040.29741500.16791347X-RAY DIFFRACTION100
3.7504-3.9210.2241430.16781388X-RAY DIFFRACTION100
3.921-4.12760.21241520.15321384X-RAY DIFFRACTION100
4.1276-4.38610.19211540.14491368X-RAY DIFFRACTION100
4.3861-4.72440.18751540.13441361X-RAY DIFFRACTION99
4.7244-5.19940.19921620.17181358X-RAY DIFFRACTION100
5.1994-5.95050.21221520.18691355X-RAY DIFFRACTION99
5.9505-7.49240.20751450.22611357X-RAY DIFFRACTION99
7.4924-47.98510.24271580.19691316X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 2.4985 Å / Origin y: 38.1651 Å / Origin z: 50.324 Å
111213212223313233
T0.2769 Å2-0.0766 Å2-0.0145 Å2-0.0226 Å20.0001 Å2--0.1803 Å2
L1.6863 °2-0.0878 °20.4449 °2-1.8659 °2-0.3388 °2--1.63 °2
S-0.4148 Å °0.3883 Å °0.2814 Å °0.2027 Å °0.3425 Å °0.6235 Å °-0.3942 Å °0.2246 Å °0.0022 Å °
Refinement TLS groupSelection details: all

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