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- PDB-5zyq: The Structure of Human PAF1/CTR9 complex -

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Basic information

Entry
Database: PDB / ID: 5zyq
TitleThe Structure of Human PAF1/CTR9 complex
ComponentsRNA polymerase-associated protein CTR9 homolog,RNA polymerase II-associated factor 1 homolog
KeywordsTRANSCRIPTION / Complex / TPR
Function / homology
Function and homology information


blastocyst growth / inner cell mass cell differentiation / Cdc73/Paf1 complex / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / blastocyst hatching / positive regulation of cell cycle G1/S phase transition / trophectodermal cell differentiation / mRNA 3'-end processing / negative regulation of gene expression, epigenetic ...blastocyst growth / inner cell mass cell differentiation / Cdc73/Paf1 complex / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / blastocyst hatching / positive regulation of cell cycle G1/S phase transition / trophectodermal cell differentiation / mRNA 3'-end processing / negative regulation of gene expression, epigenetic / stem cell population maintenance / interleukin-6-mediated signaling pathway / RNA polymerase II complex binding / cell surface receptor signaling pathway via JAK-STAT / protein localization to nucleus / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / SH2 domain binding / transcription elongation by RNA polymerase II / euchromatin / fibrillar center / Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to lipopolysaccharide / nuclear speck / intracellular membrane-bounded organelle / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / cytoplasm
Similarity search - Function
RNA polymerase-associated protein Ctr9 / RNA polymerase II associated factor Paf1 / Paf1 / 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
RNA polymerase-associated protein CTR9 homolog / RNA polymerase II-associated factor 1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.531 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 1.2Mar 27, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase-associated protein CTR9 homolog,RNA polymerase II-associated factor 1 homolog


Theoretical massNumber of molelcules
Total (without water)36,3741
Polymers36,3741
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14960 Å2
Unit cell
Length a, b, c (Å)82.415, 82.415, 145.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein RNA polymerase-associated protein CTR9 homolog,RNA polymerase II-associated factor 1 homolog / SH2 domain-binding protein 1 / hPAF1 / Pancreatic differentiation protein 2


Mass: 36374.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fusion protein of residues 1-249 from protein (UNP Q6PD62) and residues 57-116 from PAF1 (RNA polymerase II-associated factor 1 homolog, UNP Q8N7H5)
Source: (gene. exp.) Homo sapiens (human) / Gene: CTR9, KIAA0155, SH2BP1, PAF1, PD2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6PD62, UniProt: Q8N7H5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.93 Å3/Da / Density % sol: 68.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl, pH 8.0, 27.5% PEG 400, 6.875% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 17813 / % possible obs: 100 % / Redundancy: 9.9 % / Rpim(I) all: 0.022 / Net I/σ(I): 28.9
Reflection shellResolution: 2.53→2.57 Å / Num. unique obs: 964 / Rpim(I) all: 0.208

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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: 2.531→41.207 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.99
RfactorNum. reflection% reflection
Rfree0.2402 863 4.84 %
Rwork0.2018 --
obs0.2037 17813 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.531→41.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 0 103 2379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092313
X-RAY DIFFRACTIONf_angle_d1.0783122
X-RAY DIFFRACTIONf_dihedral_angle_d18.5831426
X-RAY DIFFRACTIONf_chiral_restr0.055353
X-RAY DIFFRACTIONf_plane_restr0.006406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5305-2.6890.2402810.21961859X-RAY DIFFRACTION61
2.689-2.89660.29931400.24332868X-RAY DIFFRACTION95
2.8966-3.1880.24811580.23483032X-RAY DIFFRACTION100
3.188-3.6490.30241430.22413038X-RAY DIFFRACTION100
3.649-4.59650.2261670.1793040X-RAY DIFFRACTION100
4.5965-41.21290.19791740.17373113X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.1453 Å / Origin y: 34.1302 Å / Origin z: 78.6203 Å
111213212223313233
T0.6318 Å20.3887 Å20.0602 Å2-0.2548 Å2-0.0512 Å2--0.1723 Å2
L0.9518 °20.0466 °2-0.7318 °2-1.4349 °20.1613 °2--1.2768 °2
S0.0658 Å °0.0176 Å °-0.3587 Å °-0.0602 Å °-0.2367 Å °-0.3618 Å °0.5155 Å °0.6413 Å °-0.189 Å °
Refinement TLS groupSelection details: all

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