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- PDB-6af0: Structure of Ctr9, Paf1 and Cdc73 ternary complex from Myceliopht... -

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Basic information

Entry
Database: PDB / ID: 6af0
TitleStructure of Ctr9, Paf1 and Cdc73 ternary complex from Myceliophthora thermophila
Components
  • Cdc73 protein
  • Ctr9 protein
  • Paf1 protein
KeywordsTRANSCRIPTION / Transcription elongation / Paf1 / Ctr9 / Cdc73 / crystal structure
Function / homology
Function and homology information


: / Cdc73/Paf1 complex / transcription elongation by RNA polymerase II / regulation of DNA-templated transcription
Similarity search - Function
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 / RNA polymerase II associated factor Paf1 / Paf1 / Tetratricopeptide repeat / : / Tetratricopeptide repeat ...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 / RNA polymerase II associated factor Paf1 / Paf1 / Tetratricopeptide repeat / : / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
CDC73_C domain-containing protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.88 Å
AuthorsWang, Z. / Deng, P. / Zhou, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570729 China
National Natural Science Foundation of China31370719 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Transcriptional elongation factor Paf1 core complex adopts a spirally wrapped solenoidal topology.
Authors: Deng, P. / Zhou, Y. / Jiang, J. / Li, H. / Tian, W. / Cao, Y. / Qin, Y. / Kim, J. / Roeder, R.G. / Patel, D.J. / Wang, Z.
History
DepositionAug 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Ctr9 protein
P: Paf1 protein
C: Cdc73 protein


Theoretical massNumber of molelcules
Total (without water)126,8953
Polymers126,8953
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15930 Å2
ΔGint-96 kcal/mol
Surface area49980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.867, 237.789, 62.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ctr9 protein


Mass: 106251.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus)
Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2305158 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2QC65
#2: Protein Paf1 protein


Mass: 12983.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus)
Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2303763 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2QDK9
#3: Protein Cdc73 protein


Mass: 7659.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus)
Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2298931 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2Q3X1

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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: 2.94 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium phosphate dibasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.88→118.89 Å / Num. obs: 34480 / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 24.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1718 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.88→118.89 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.885 / SU B: 23.517 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30929 1729 5 %RANDOM
Rwork0.24522 ---
obs0.24829 32640 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.026 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å2-0 Å2
2---0.2 Å2-0 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 2.88→118.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8372 0 0 0 8372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198541
X-RAY DIFFRACTIONr_bond_other_d0.0060.028238
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.97311546
X-RAY DIFFRACTIONr_angle_other_deg0.837318952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80851048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30924.029417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.548151510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5341571
X-RAY DIFFRACTIONr_chiral_restr0.0710.21250
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219706
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021953
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.0599.0484210
X-RAY DIFFRACTIONr_mcbond_other6.0519.0484209
X-RAY DIFFRACTIONr_mcangle_it9.10113.5765252
X-RAY DIFFRACTIONr_mcangle_other9.113.5775253
X-RAY DIFFRACTIONr_scbond_it6.4619.5394331
X-RAY DIFFRACTIONr_scbond_other6.4619.544332
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.00614.0996295
X-RAY DIFFRACTIONr_long_range_B_refined14.2173.74710592
X-RAY DIFFRACTIONr_long_range_B_other14.2173.75110593
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.884→2.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 110 -
Rwork0.401 2244 -
obs--92.93 %

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