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- PDB-5ohq: Crystal structure of the KOW6-KOW7 domain of human DSIF -

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Basic information

Entry
Database: PDB / ID: 5ohq
TitleCrystal structure of the KOW6-KOW7 domain of human DSIF
ComponentsTranscription elongation factor SPT5
KeywordsTRANSCRIPTION / RNA polymerase II / transcription elongation
Function / homology
Function and homology information


negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / positive regulation of DNA-templated transcription, elongation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex ...negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / positive regulation of DNA-templated transcription, elongation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / positive regulation of macroautophagy / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / protein heterodimerization activity / mRNA binding / chromatin binding / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Spt5, KOW domain repeat 6 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic ...Spt5, KOW domain repeat 6 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
Transcription elongation factor SPT5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.098 Å
AuthorsBernecky, C. / Plitzko, J.M. / Cramer, P.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationSFB860, SPP1935 Germany
European Research CouncilTRANSREGULON Germany
Volkswagen Foundation Germany
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.
Authors: Carrie Bernecky / Jürgen M Plitzko / Patrick Cramer /
Abstract: During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA ...During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4 Å. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis.
History
DepositionJul 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: pdbx_database_related / pdbx_struct_special_symmetry
Item: _pdbx_database_related.content_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2703
Polymers12,2121
Non-polymers582
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-16 kcal/mol
Surface area6460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.091, 75.657, 96.749
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-989-

ARG

21A-1069-

LEU

31A-1386-

HOH

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Components

#1: Protein Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing ...hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 12211.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: O00267
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M bis-tris propane pH 7, 3 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987357022 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987357022 Å / Relative weight: 1
ReflectionResolution: 1.098→48.375 Å / Num. obs: 93250 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 6.163 % / Biso Wilson estimate: 12.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.035 / Χ2: 1.033 / Net I/σ(I): 27.7 / Num. measured all: 574723
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.162.740.1634.32255121636693100.9770.20356.9
1.16-1.245.2260.1448.397463715461142820.990.1692.4
1.24-1.346.7220.10913.389685114422144090.9960.11899.9
1.34-1.476.5280.0720.258596513231131690.9970.07799.5
1.47-1.657.0770.04931.268470911967119690.9990.053100
1.65-1.96.840.03742.27215210575105490.9990.0499.8
1.9-2.336.8630.03154.9361125893289070.9990.03499.7
2.33-3.297.0970.02861.0348914689368920.9990.03100
3.29-48.3756.6060.02962.2524858379937630.9980.03299.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata scaling
SHELXDEphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.098→48.374 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1401 4760 5.11 %
Rwork0.1224 88464 -
obs0.1233 93224 91.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.6 Å2 / Biso mean: 20.851 Å2 / Biso min: 9.75 Å2
Refinement stepCycle: final / Resolution: 1.098→48.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms849 0 2 243 1094
Biso mean--26.74 38.38 -
Num. residues----110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011015
X-RAY DIFFRACTIONf_angle_d1.1631413
X-RAY DIFFRACTIONf_chiral_restr0.092179
X-RAY DIFFRACTIONf_plane_restr0.006180
X-RAY DIFFRACTIONf_dihedral_angle_d20.082422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0975-1.110.2059670.20851175124238
1.11-1.1230.2158870.17281530161747
1.123-1.13670.20811060.14841798190456
1.1367-1.15110.14051290.14222125225467
1.1511-1.16630.14191200.13542571269178
1.1663-1.18220.15611750.12532651282683
1.1822-1.19910.15981440.12942875301990
1.1991-1.2170.15461740.11953044321895
1.217-1.23610.14461710.115932163387100
1.2361-1.25630.1631750.105932073382100
1.2563-1.2780.14271570.101832163373100
1.278-1.30120.12742320.110431943426100
1.3012-1.32630.11851470.102932023349100
1.3263-1.35330.12991920.100432353427100
1.3533-1.38280.1161660.09931923358100
1.3828-1.41490.14251720.095832023374100
1.4149-1.45030.1131560.09713226338299
1.4503-1.48950.12661470.097932543401100
1.4895-1.53340.12141430.093132463389100
1.5334-1.58290.11871880.088831673355100
1.5829-1.63940.11721640.098632283392100
1.6394-1.70510.12131640.104732343398100
1.7051-1.78270.14531890.115131793368100
1.7827-1.87670.13031560.114432373393100
1.8767-1.99430.12031520.11083219337199
1.9943-2.14820.121770.108332133390100
2.1482-2.36440.12312010.111431793380100
2.3644-2.70650.14341600.13932553415100
2.7065-3.40980.15331890.139331953384100
3.4098-48.42150.16431600.14823199335999

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