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- PDB-8j8q: Structure of the four-component Paf1 complex from Saccharomyces e... -

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Basic information

Entry
Database: PDB / ID: 8j8q
TitleStructure of the four-component Paf1 complex from Saccharomyces eubayanus
Components
  • CDC73-like protein
  • CTR9-like protein
  • PAF1-like protein
  • RTF1-like protein
KeywordsTRANSCRIPTION / transcription elongation factor / the polymerase associated factor 1 (Paf1) complex
Function / homology
Function and homology information


Cdc73/Paf1 complex / transcription elongation by RNA polymerase II / regulation of DNA-templated transcription / protein-containing complex / DNA binding / nucleus
Similarity search - Function
Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / RNA polymerase II associated factor Paf1 / Paf1 / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal ...Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / RNA polymerase II associated factor Paf1 / Paf1 / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / RNA pol II accessory factor, Cdc73 family, C-terminal / Tetratricopeptide repeat / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
CDC73-like protein / CTR9-like protein / RTF1-like protein / PAF1-like protein
Similarity search - Component
Biological speciesSaccharomyces eubayanus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.11 Å
AuthorsWang, Z. / Qin, Y. / Zhou, Y. / Cao, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870725 China
National Natural Science Foundation of China (NSFC)32125008 China
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Basis of the Transcriptional Elongation Factor Paf1 Core Complex from Saccharomyces eubayanus .
Authors: Qin, Y. / Zhou, Y. / Cao, Y. / Ren, Y. / Deng, P. / Jiang, J. / Wang, Z.
History
DepositionMay 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: CTR9-like protein
P: PAF1-like protein
R: RTF1-like protein
A: CDC73-like protein


Theoretical massNumber of molelcules
Total (without water)136,3704
Polymers136,3704
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20710 Å2
ΔGint-139 kcal/mol
Surface area52700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.634, 89.173, 128.072
Angle α, β, γ (deg.)90.000, 97.085, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein CTR9-like protein


Mass: 105524.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_2263 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RHL9
#2: Protein PAF1-like protein


Mass: 12841.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_1302 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RM45
#3: Protein RTF1-like protein


Mass: 9468.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_1738 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RIY1
#4: Protein CDC73-like protein


Mass: 8535.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces eubayanus (yeast) / Gene: DI49_3914 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8RF82
Has ligand of interestN
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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium citrate tribasic pH 7.0; 25% w/v Polyethylene glyco 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX170-HS / Detector: CCD / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 28686 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.08 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→3.15 Å / Rmerge(I) obs: 1.116 / Num. unique obs: 1421

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.11→27.07 Å / SU ML: 0.3946 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.1256 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.278 1428 4.98 %
Rwork0.237 27258 -
obs0.239 28686 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.94 Å2
Refinement stepCycle: LAST / Resolution: 3.11→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8756 0 0 0 8756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00998908
X-RAY DIFFRACTIONf_angle_d1.136412002
X-RAY DIFFRACTIONf_chiral_restr0.09451346
X-RAY DIFFRACTIONf_plane_restr0.00571535
X-RAY DIFFRACTIONf_dihedral_angle_d23.20063410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.220.3271300.2862469X-RAY DIFFRACTION90.78
3.22-3.340.33591430.26582726X-RAY DIFFRACTION99.76
3.34-3.50.27891350.25332754X-RAY DIFFRACTION99.97
3.5-3.680.29251380.23682770X-RAY DIFFRACTION99.93
3.68-3.910.26731490.22722743X-RAY DIFFRACTION99.79
3.91-4.210.26121460.20722745X-RAY DIFFRACTION98.8
4.21-4.630.24541410.19582726X-RAY DIFFRACTION99.79
4.63-5.30.23761380.22272774X-RAY DIFFRACTION99.97
5.3-6.660.29291730.28712735X-RAY DIFFRACTION99.08
6.66-27.070.28041350.23652816X-RAY DIFFRACTION98.79
Refinement TLS params.Method: refined / Origin x: 17.1641781077 Å / Origin y: 33.1082699959 Å / Origin z: -5.91981776579 Å
111213212223313233
T0.302534475995 Å2-0.093291451354 Å2-0.0320672068514 Å2-0.0401333337151 Å2-0.0253018774165 Å2--0.206131168594 Å2
L1.8186692188 °2-0.451480228839 °20.29691334372 °2-0.72269372849 °2-0.114652917328 °2--1.52622307229 °2
S0.167408286899 Å °0.225106226159 Å °-0.329393712486 Å °-0.338622155129 Å °-0.011221345475 Å °0.231605296402 Å °0.18892003357 Å °-0.563723323469 Å °-0.083960289343 Å °
Refinement TLS groupSelection details: all

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