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- PDB-5vko: SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493 -

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Basic information

Entry
Database: PDB / ID: 5vko
TitleSPT6 tSH2-RPB1 1468-1500 pT1471, pS1493
Components
  • DNA-directed RNA polymerase II subunit RPB1
  • Transcription elongation factor SPT6
KeywordsTRANSCRIPTION / SH2 domain phosphorylation histone chaperone transcription
Function / homology
Function and homology information


carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / nucleosome organization / transcription elongation-coupled chromatin remodeling / Processing of Capped Intron-Containing Pre-mRNA / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex ...carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / nucleosome organization / transcription elongation-coupled chromatin remodeling / Processing of Capped Intron-Containing Pre-mRNA / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / Dual incision in TC-NER / RNA polymerase II, core complex / translesion synthesis / RNA polymerase II activity / nucleosome binding / transcription elongation factor complex / transcription antitermination / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / euchromatin / cytoplasmic stress granule / DNA-directed RNA polymerase / nucleosome assembly / chromatin organization / histone binding / transcription by RNA polymerase II / chromatin remodeling / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleus / metal ion binding
Similarity search - Function
: / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 ...: / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / RuvA domain 2-like / SH2 domain / SHC Adaptor Protein / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / DNA-directed RNA polymerase II subunit RPB1 / Transcription elongation factor SPT6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSdano, M.A. / Whitby, F.G. / Hill, C.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM116560 United States
CitationJournal: Elife / Year: 2017
Title: A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription.
Authors: Sdano, M.A. / Fulcher, J.M. / Palani, S. / Chandrasekharan, M.B. / Parnell, T.J. / Whitby, F.G. / Formosa, T. / Hill, C.P.
History
DepositionApr 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jan 1, 2020Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 2.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Transcription elongation factor SPT6
B: DNA-directed RNA polymerase II subunit RPB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8033
Polymers28,7432
Non-polymers601
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Fluorescence polarization and far western assays were used to validate assembly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-17 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.448, 102.102, 115.743
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1614-

HOH

21A-1689-

HOH

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Components

#1: Protein Transcription elongation factor SPT6 / Chromatin elongation factor SPT6


Mass: 25065.430 Da / Num. of mol.: 1 / Fragment: UNP residues 1247-1451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SPT6, CRE2, SSN20, YGR116W, G6169 / Production host: Escherichia coli (E. coli) / References: UniProt: P23615
#2: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 3677.786 Da / Num. of mol.: 1 / Fragment: UNP residues 1468-1500 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04050, DNA-directed RNA polymerase
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% iso-Propanol, 0.1 M Na Hepes pH 7.5, 20% PEG 4000
Temp details: constant temp

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 14, 2016 / Details: VeriMax-HR confocal optic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→32.453 Å / Num. obs: 23766 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 30.68 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.035 / Rrim(I) all: 0.099 / Χ2: 0.977 / Net I/σ(I): 13 / Num. measured all: 186789
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.865.21.11923270.6410.5181.2380.84999
1.86-1.947.30.96623550.8320.3861.0410.94100
1.94-2.038.10.73923390.9190.2810.7911.012100
2.03-2.138.20.47823400.9550.180.5111.059100
2.13-2.278.30.35223570.9730.1320.3771.053100
2.27-2.448.20.26423450.9830.0990.2821.023100
2.44-2.698.20.17923690.990.0670.1920.983100
2.69-3.088.30.11224100.9960.0420.120.929100
3.08-3.888.30.05724060.9980.0210.0610.913100
3.88-408.50.04125180.9990.0150.0440.95799.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.17 Å32.45 Å
Translation5.17 Å32.45 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.7.15phasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PSJ

3psj


Resolution: 1.8→32.453 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1975 1999 8.43 %
Rwork0.1619 21723 -
obs0.1649 23722 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.14 Å2 / Biso mean: 44.6542 Å2 / Biso min: 19.22 Å2
Refinement stepCycle: final / Resolution: 1.8→32.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 12 171 2109
Biso mean--87.23 45.84 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092001
X-RAY DIFFRACTIONf_angle_d1.0132714
X-RAY DIFFRACTIONf_chiral_restr0.058287
X-RAY DIFFRACTIONf_plane_restr0.007351
X-RAY DIFFRACTIONf_dihedral_angle_d11.0861203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.84510.38911380.30951498163696
1.8451-1.8950.31341400.260815221662100
1.895-1.95080.26581410.245115221663100
1.9508-2.01370.25231400.198615351675100
2.0137-2.08570.22881410.175815381679100
2.0857-2.16920.2031430.166315381681100
2.1692-2.26790.22531420.163915481690100
2.2679-2.38740.20691410.164215321673100
2.3874-2.53690.20441420.16615531695100
2.5369-2.73270.2351430.167415481691100
2.7327-3.00750.22641450.166615701715100
3.0075-3.44230.21441430.156215651708100
3.4423-4.33530.15721470.130315921739100
4.3353-32.4580.15271530.15516621815100
Refinement TLS params.Method: refined / Origin x: -72.464 Å / Origin y: 117.5603 Å / Origin z: 2.393 Å
111213212223313233
T0.2112 Å20 Å20.0143 Å2-0.1952 Å2-0.0173 Å2--0.26 Å2
L1.1471 °20.0476 °20.0849 °2-0.9035 °20.035 °2--1.5914 °2
S-0.0827 Å °0.0102 Å °-0.1794 Å °-0.0422 Å °0.0723 Å °-0.087 Å °0.1534 Å °0.0948 Å °0.0356 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1250 - 1450
2X-RAY DIFFRACTION1allB1469 - 1499
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 199

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