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- PDB-4m6t: Structure of human Paf1 and Leo1 complex -

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Basic information

Entry
Database: PDB / ID: 4m6t
TitleStructure of human Paf1 and Leo1 complex
ComponentsRNA polymerase II-associated factor 1 homolog, Linker, RNA polymerase-associated protein LEO1
KeywordsTranscription Regulator / Paf1-Leo1 subcomplex / transcription elongator
Function / homology
Function and homology information


RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / positive regulation of cell cycle G1/S phase transition / mRNA 3'-end processing / stem cell population maintenance / RNA polymerase II complex binding / protein localization to nucleus / RNA Polymerase II Transcription Elongation ...RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / positive regulation of cell cycle G1/S phase transition / mRNA 3'-end processing / stem cell population maintenance / RNA polymerase II complex binding / protein localization to nucleus / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / Wnt signaling pathway / fibrillar center / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to lipopolysaccharide / intracellular membrane-bounded organelle / centrosome / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Leo1-like protein / Leo1-like protein / RNA polymerase II associated factor Paf1 / Paf1
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / RNA polymerase II-associated factor 1 homolog / RNA polymerase-associated protein LEO1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.498 Å
AuthorsShen, Y. / Qin, X.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural insights into Paf1 complex assembly and histone binding
Authors: Chu, X. / Qin, X. / Xu, H. / Li, L. / Wang, Z. / Li, F. / Xie, X. / Zhou, H. / Shen, Y. / Long, J.
History
DepositionAug 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II-associated factor 1 homolog, Linker, RNA polymerase-associated protein LEO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6692
Polymers21,2711
Non-polymers3981
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA polymerase II-associated factor 1 homolog, Linker, RNA polymerase-associated protein LEO1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)130,01612
Polymers127,6256
Non-polymers2,3916
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area23940 Å2
ΔGint-161 kcal/mol
Surface area46220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.168, 115.168, 157.437
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein RNA polymerase II-associated factor 1 homolog, Linker, RNA polymerase-associated protein LEO1


Mass: 21270.889 Da / Num. of mol.: 1
Fragment: UNP residues 170-250 of Paf1, UNP residues 370-462 of LEO1
Source method: isolated from a genetically manipulated source
Details: chimera of RNA polymerase II-associated factor 1 homolog, Linker, RNA polymerase-associated protein LEO1
Source: (gene. exp.) Homo sapiens (human) / Gene: PAF1, LEO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N7H5, UniProt: Q8WVC0
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.72 Å3/Da / Density % sol: 73.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5M sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.498→50 Å / Num. all: 14138 / Num. obs: 14136 / % possible obs: 99.75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 43.6 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.498→38.788 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7713 / SU ML: 0.8 / σ(F): 1.35 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 712 5.04 %RANDOM
Rwork0.2324 ---
obs0.2341 14136 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.536 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 85.56 Å2 / Biso mean: 45.8081 Å2 / Biso min: 27.55 Å2
Baniso -1Baniso -2Baniso -3
1-7.3181 Å20 Å2-0 Å2
2--7.3181 Å2-0 Å2
3----14.6363 Å2
Refinement stepCycle: LAST / Resolution: 2.498→38.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 27 4 1404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081434
X-RAY DIFFRACTIONf_angle_d1.1821944
X-RAY DIFFRACTIONf_chiral_restr0.084210
X-RAY DIFFRACTIONf_plane_restr0.005252
X-RAY DIFFRACTIONf_dihedral_angle_d19.909517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4978-2.69060.37661580.33712592275099
2.6906-2.96130.30061400.288426682808100
2.9613-3.38960.27911540.24426662820100
3.3896-4.26970.23561260.192927022828100
4.2697-38.79240.24611340.219127962930100

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