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- PDB-6er0: 6th KOW domain of human hSpt5 -

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Basic information

Entry
Database: PDB / ID: 6er0
Title6th KOW domain of human hSpt5
ComponentsTranscription elongation factor SPT5
KeywordsTRANSCRIPTION / DSIF. transcription elongation / hSpt5
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 / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / 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)
MethodSOLUTION NMR / simulated annealing
AuthorsHahn, L. / Schweimer, K. / Roesch, P. / Woehrl, B.M.
CitationJournal: Sci Rep / Year: 2018
Title: Structure and nucleic acid binding properties of KOW domains 4 and 6-7 of human transcription elongation factor DSIF.
Authors: Zuber, P.K. / Hahn, L. / Reinl, A. / Schweimer, K. / Knauer, S.H. / Gottesman, M.E. / Rosch, P. / Wohrl, B.M.
History
DepositionOct 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription elongation factor SPT5


Theoretical massNumber of molelcules
Total (without water)13,8581
Polymers13,8581
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7100 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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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: 13857.621 Da / Num. of mol.: 1 / Fragment: KOW6 domain, UNP residues 961-1087
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00267

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HNCA
1151isotropic13D HN(CA)CB
1141isotropic13D CBCA(CO)NH
1131isotropic13D C(CO)NH
1121isotropic13D (H)CCH-TOCSY
1111isotropic13D CCH-TOCSY
1101isotropic23D 1H-15N NOESY
191isotropic23D 1H-13C NOESY aliphatic
181isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.44 mM [U-99% 13C; U-99% 15N] KOW6, 20 mM sodium phosphate, 20 mM sodium chloride, 0.5 mM DTT, 90% H2O/10% D2O
Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.44 mMKOW6[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
20 mMsodium chloridenatural abundance1
0.5 mMDTTnatural abundance1
Sample conditionsIonic strength: 40 mM / Label: condition_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III7001cryoprobe
Bruker AVANCE IIIBrukerAVANCE III10002cryoprobe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 15

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