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- PDB-5oho: Crystal structure of the KOWx-KOW4 domain of human DSIF -

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Basic information

Entry
Database: PDB / ID: 5oho
TitleCrystal structure of the KOWx-KOW4 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 / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / 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 / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / 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 / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / 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 / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / 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 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal ...Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, fourth KOW domain / 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 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / 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: 1.601 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 / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription elongation factor SPT5
B: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1987
Polymers25,7942
Non-polymers4045
Water4,576254
1
A: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0813
Polymers12,8971
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1174
Polymers12,8971
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.286, 54.403, 73.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 12896.992 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 1.0 M tri-sodium citrate dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003056744 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003056744 Å / Relative weight: 1
ReflectionResolution: 1.6→43.635 Å / Num. obs: 50856 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.76 % / Biso Wilson estimate: 31.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.051 / Χ2: 1.273 / Net I/σ(I): 15.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.76.4661.3360.9481200.4851.45298.7
1.7-1.827.0020.6942.177700.810.74999.9
1.82-1.966.8450.334.7971890.9490.35799.9
1.96-2.156.5610.1619.8866400.9880.175100
2.15-2.47.0520.10117.1860020.9950.109100
2.4-2.776.7310.0724.1452980.9970.076100
2.77-3.396.6090.04338.7744760.9990.04699.9
3.39-4.786.8130.03351.1434460.9990.03599.9
4.78-43.6356.810.02753.7219150.9990.02999.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.601→43.635 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.55
RfactorNum. reflection% reflection
Rfree0.2213 2507 4.93 %
Rwork0.1745 --
obs0.1767 50852 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.99 Å2 / Biso mean: 42.3488 Å2 / Biso min: 23.11 Å2
Refinement stepCycle: final / Resolution: 1.601→43.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 25 254 2091
Biso mean--55 54.35 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061917
X-RAY DIFFRACTIONf_angle_d0.8622586
X-RAY DIFFRACTIONf_chiral_restr0.057287
X-RAY DIFFRACTIONf_plane_restr0.005335
X-RAY DIFFRACTIONf_dihedral_angle_d18.1491158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6012-1.6320.39221580.33712559271796
1.632-1.66530.35981440.325226752819100
1.6653-1.70150.29841360.289927202856100
1.7015-1.74110.28831420.264326982840100
1.7411-1.78460.32041280.257626882816100
1.7846-1.83290.27691410.244426712812100
1.8329-1.88680.32581370.232827092846100
1.8868-1.94770.28631640.207426492813100
1.9477-2.01730.22961440.190727162860100
2.0173-2.09810.20391280.184227102838100
2.0981-2.19360.20241270.18426902817100
2.1936-2.30920.25251140.194327092823100
2.3092-2.45390.25071620.203926762838100
2.4539-2.64330.26911430.209226942837100
2.6433-2.90930.24411190.18626982817100
2.9093-3.33010.2031570.162726862843100
3.3301-4.19510.16951220.128627192841100
4.1951-43.65180.19491410.153826782819100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.69931.2923-0.71622.39030.54131.20870.08020.0951-0.2758-0.26170.1182-0.1443-0.26080.036800.29110.0289-0.07160.2818-0.02880.297315.702764.725622.8543
20.9783-0.0767-0.48051.3642-0.811.290.04340.6780.118-0.2106-0.0015-0.3255-0.2510.6816-0.00020.27410.0052-0.01080.4026-0.0190.316222.563566.238921.3771
30.1250.2612-0.03580.308-0.1840.07160.1964-0.26610.66390.572-0.13150.46110.21780.0194-0.00210.4309-0.043-0.01980.3961-0.02450.44126.016464.49827.3113
41.67410.22510.15172.8621.15141.78150.0980.267-0.3970.32490.1067-0.26010.54720.1426-0.00090.44460.0353-0.06780.2984-0.01150.31174.460249.757717.2323
52.11312.01120.0221.97080.68782.27730.18380.3737-0.3080.18450.1699-0.68310.49010.50370.02950.35920.1019-0.1080.3117-0.05630.389610.417252.634217.1767
64.21442.0111-0.384.33062.34113.0584-0.06290.01880.2825-0.5283-0.1017-0.0401-0.1468-0.0014-0.00430.1765-0.01210.00290.328-0.07780.2834-6.704860.13337.7925
71.0031-0.7903-0.36820.46620.2740.06680.35350.2975-0.6039-0.02280.25-0.77591.17010.25890.00220.7475-0.0486-0.14470.3813-0.02850.4442-3.790446.859430.3823
83.60011.9657-0.15593.07352.56083.8996-0.18260.1194-0.25890.0218-0.04410.10460.2537-0.1433-0.00030.2753-0.0277-0.00360.23330.00890.2148-18.607544.297636.7247
90.0291-0.0077-0.05620.0502-0.00610.1466-0.1413-0.5745-0.9396-0.31550.80410.6355-0.1998-0.58580.00330.43780.0024-0.19740.3540.04340.6655-26.307157.075432.1734
101.87390.1344-0.49041.01830.84720.8414-0.3398-0.09580.2461-0.23860.06770.14470.1212-0.4423-0.00020.3206-0.0178-0.04890.2821-0.0160.3271-19.828648.684239.004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 534 through 553 )A534 - 553
2X-RAY DIFFRACTION2chain 'A' and (resid 554 through 574 )A554 - 574
3X-RAY DIFFRACTION3chain 'A' and (resid 575 through 584 )A575 - 584
4X-RAY DIFFRACTION4chain 'A' and (resid 585 through 617 )A585 - 617
5X-RAY DIFFRACTION5chain 'A' and (resid 618 through 646 )A618 - 646
6X-RAY DIFFRACTION6chain 'B' and (resid 534 through 574 )B534 - 574
7X-RAY DIFFRACTION7chain 'B' and (resid 575 through 584 )B575 - 584
8X-RAY DIFFRACTION8chain 'B' and (resid 585 through 625 )B585 - 625
9X-RAY DIFFRACTION9chain 'B' and (resid 626 through 630 )B626 - 630
10X-RAY DIFFRACTION10chain 'B' and (resid 631 through 646 )B631 - 646

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