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- PDB-3h7h: Crystal structure of the human transcription elongation factor DS... -

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Basic information

Entry
Database: PDB / ID: 3h7h
TitleCrystal structure of the human transcription elongation factor DSIF, hSpt4/hSpt5 (176-273)
Components
  • Transcription elongation factor SPT4
  • Transcription elongation factor SPT5
KeywordsTRANSCRIPTION / helices surrounding beta sheet / Activator / Metal-binding / Nucleus / Repressor / Transcription regulation / Zinc-finger / Methylation / Phosphoprotein
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 / positive regulation of DNA-templated transcription, elongation / 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 / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / 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 / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / 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 / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / chromatin organization / protein heterodimerization activity / mRNA binding / chromatin binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Herpes Virus-1 - #210 / NusG, N-terminal domain / Spt5, KOW domain repeat 6 / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 ...Herpes Virus-1 - #210 / NusG, N-terminal domain / Spt5, KOW domain repeat 6 / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / 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 / Herpes Virus-1 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW / KOW motif / Ribosomal protein L2, domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Transcription elongation factor SPT5 / Transcription elongation factor SPT4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsWenzel, S. / Wohrl, B.M. / Rosch, P. / Martins, B.M.
CitationJournal: Biochem.J. / Year: 2010
Title: Crystal structure of the human transcription elongation factor DSIF hSpt4 subunit in complex with the hSpt5 dimerization interface
Authors: Wenzel, S. / Martins, B.M. / Rosch, P. / Wohrl, B.M.
History
DepositionApr 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Transcription elongation factor SPT4
B: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4944
Polymers25,3502
Non-polymers1442
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-24 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.096, 52.091, 97.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription elongation factor SPT4 / hSPT4 / DRB sensitivity-inducing factor small subunit / DSIF small subunit / DSIF p14


Mass: 13395.382 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETGB_1a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P63272
#2: Protein Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / DSIF p160 / Tat- ...hSPT5 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / DSIF p160 / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 11954.917 Da / Num. of mol.: 1 / Fragment: UNP residues 176-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O00267
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, PEG 3350, Tris/HCl, beta-mercaptoethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.283 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 28930

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Processing

Software
NameClassification
XDSdata scaling
SHELXSphasing
REFMACrefinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.55→19.11 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.222 1523 5%
Rwork0.186 --
obs-28930 -
Displacement parametersBiso mean: 14.36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.62 Å20 Å2
3----0.61 Å2
Refine analyzeLuzzati coordinate error obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.55→19.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 5 196 1893
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d1.277
LS refinement shellResolution: 1.55→1.59 Å
RfactorNum. reflection
Rfree0.256 98
Rwork0.222 -
obs-1870

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