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- PDB-7faw: Structure of LW domain from Yeast -

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Basic information

Entry
Database: PDB / ID: 7faw
TitleStructure of LW domain from Yeast
ComponentsTranscription elongation factor S-II
KeywordsTRANSCRIPTION / LW / Paf1C
Function / homology
Function and homology information


RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / TP53 Regulates Transcription of DNA Repair Genes / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / Dual incision in TC-NER / positive regulation of RNA polymerase II transcription preinitiation complex assembly ...RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / TP53 Regulates Transcription of DNA Repair Genes / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / Dual incision in TC-NER / positive regulation of RNA polymerase II transcription preinitiation complex assembly / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription antitermination / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) ...Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / Zinc finger TFIIS-type signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription elongation factor S-II
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.438 Å
AuthorsLiao, S. / Gao, J. / Tu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31500601 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural basis for evolutionarily conserved interactions between TFIIS and Paf1C.
Authors: Gao, J. / Jishage, M. / Wang, Y. / Wang, R. / Chen, M. / Zhu, Z. / Zhang, J. / Diwu, Y. / Xu, C. / Liao, S. / Roeder, R.G. / Tu, X.
History
DepositionJul 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription elongation factor S-II
B: Transcription elongation factor S-II
C: Transcription elongation factor S-II


Theoretical massNumber of molelcules
Total (without water)29,4013
Polymers29,4013
Non-polymers00
Water68538
1
A: Transcription elongation factor S-II


Theoretical massNumber of molelcules
Total (without water)9,8001
Polymers9,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription elongation factor S-II


Theoretical massNumber of molelcules
Total (without water)9,8001
Polymers9,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription elongation factor S-II


Theoretical massNumber of molelcules
Total (without water)9,8001
Polymers9,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.014, 91.568, 118.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 4 or (resid 5...
21(chain B and (resid 1 through 3 or (resid 4...
31(chain C and (resid 1 through 4 or (resid 5...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYS(chain A and (resid 1 through 4 or (resid 5...AA1 - 41 - 4
12GLUGLUGLUGLU(chain A and (resid 1 through 4 or (resid 5...AA55
13METMETGLNGLN(chain A and (resid 1 through 4 or (resid 5...AA1 - 841 - 84
14METMETGLNGLN(chain A and (resid 1 through 4 or (resid 5...AA1 - 841 - 84
15METMETGLNGLN(chain A and (resid 1 through 4 or (resid 5...AA1 - 841 - 84
16METMETGLNGLN(chain A and (resid 1 through 4 or (resid 5...AA1 - 841 - 84
21METMETSERSER(chain B and (resid 1 through 3 or (resid 4...BB1 - 31 - 3
22LYSLYSGLUGLU(chain B and (resid 1 through 3 or (resid 4...BB4 - 54 - 5
23METMETGLNGLN(chain B and (resid 1 through 3 or (resid 4...BB1 - 841 - 84
24METMETGLNGLN(chain B and (resid 1 through 3 or (resid 4...BB1 - 841 - 84
25METMETGLNGLN(chain B and (resid 1 through 3 or (resid 4...BB1 - 841 - 84
26METMETGLNGLN(chain B and (resid 1 through 3 or (resid 4...BB1 - 841 - 84
27METMETGLNGLN(chain B and (resid 1 through 3 or (resid 4...BB1 - 841 - 84
28METMETGLNGLN(chain B and (resid 1 through 3 or (resid 4...BB1 - 841 - 84
29METMETGLNGLN(chain B and (resid 1 through 3 or (resid 4...BB1 - 841 - 84
210METMETGLNGLN(chain B and (resid 1 through 3 or (resid 4...BB1 - 841 - 84
211METMETGLNGLN(chain B and (resid 1 through 3 or (resid 4...BB1 - 841 - 84
31METMETLYSLYS(chain C and (resid 1 through 4 or (resid 5...CC1 - 41 - 4
32GLUGLUGLUGLU(chain C and (resid 1 through 4 or (resid 5...CC55
33METMETGLNGLN(chain C and (resid 1 through 4 or (resid 5...CC1 - 841 - 84
34METMETGLNGLN(chain C and (resid 1 through 4 or (resid 5...CC1 - 841 - 84
35METMETGLNGLN(chain C and (resid 1 through 4 or (resid 5...CC1 - 841 - 84
36METMETGLNGLN(chain C and (resid 1 through 4 or (resid 5...CC1 - 841 - 84

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Components

#1: Protein Transcription elongation factor S-II / DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway ...DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway regulatory protein 2


Mass: 9800.458 Da / Num. of mol.: 3 / Fragment: LW domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: DST1, PPR2, YGL043W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07273
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris, pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.438→118.07 Å / Num. obs: 24984 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Net I/σ(I): 20.2
Reflection shellResolution: 2.44→2.5 Å / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 996 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model built by rosetta

Resolution: 2.438→36.179 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 2509 10.04 %
Rwork0.2016 22475 -
obs0.2054 24984 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.01 Å2 / Biso mean: 42.4344 Å2 / Biso min: 24.54 Å2
Refinement stepCycle: final / Resolution: 2.438→36.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 0 38 2015
Biso mean---40.89 -
Num. residues----252
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A750X-RAY DIFFRACTION5.485TORSIONAL
12B750X-RAY DIFFRACTION5.485TORSIONAL
13C750X-RAY DIFFRACTION5.485TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4385-2.48540.3441400.26211271
2.4854-2.53610.29281420.23561228
2.5361-2.59120.30841380.22321238
2.5912-2.65150.25661400.2371270
2.6515-2.71780.29381400.21291253
2.7178-2.79120.2731350.2171205
2.7912-2.87330.23311460.22731290
2.8733-2.9660.27071460.23261231
2.966-3.0720.26431380.23481226
3.072-3.19490.2721450.23541294
3.1949-3.34020.31431360.23141201
3.3402-3.51620.26491380.21731269
3.5162-3.73630.23571350.20211247
3.7363-4.02440.21821420.1751270
4.0244-4.42880.18181340.15921232
4.4288-5.06810.19051360.17011260
5.0681-6.37960.26311410.22111256
6.3796-36.170.18621370.17031234
Refinement TLS params.Method: refined / Origin x: -5.1348 Å / Origin y: 8.4774 Å / Origin z: -14.2892 Å
111213212223313233
T0.2875 Å2-0.0065 Å20.0192 Å2-0.323 Å2-0.0207 Å2--0.3271 Å2
L0.3457 °2-0.0706 °2-0.0577 °2-0.4683 °20.5891 °2--0.7475 °2
S0.0515 Å °0.0638 Å °-0.0559 Å °-0.0318 Å °-0.0039 Å °0.0373 Å °0.1166 Å °-0.0877 Å °-0.0093 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 84
2X-RAY DIFFRACTION1allB1 - 84
3X-RAY DIFFRACTION1allC1 - 84
4X-RAY DIFFRACTION1allS1 - 50

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