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- PDB-4ytk: Structure of the KOW1-Linker1 domain of Transcription Elongation ... -

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Basic information

Entry
Database: PDB / ID: 4ytk
TitleStructure of the KOW1-Linker1 domain of Transcription Elongation Factor Spt5
ComponentsTranscription elongation factor SPT5
KeywordsTRANSCRIPTION / elongation / RNA processing / protein-DNA interaction.
Function / homology
Function and homology information


negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / regulation of rRNA processing / RNA polymerase I core binding / DSIF complex / snRNP binding / intracellular mRNA localization / RNA polymerase I general transcription initiation factor binding / U4 snRNA binding ...negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / regulation of rRNA processing / RNA polymerase I core binding / DSIF complex / snRNP binding / intracellular mRNA localization / RNA polymerase I general transcription initiation factor binding / U4 snRNA binding / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / spliceosomal complex assembly / RNA polymerase II complex binding / U5 snRNA binding / U2 snRNA binding / U6 snRNA binding / positive regulation of autophagy / U1 snRNA binding / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / chromosome / rRNA binding / mRNA binding / protein-containing complex binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / nucleus
Similarity search - Function
Spt5 C-terminal nonapeptide repeat binding Spt4 / 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 C-terminal nonapeptide repeat binding Spt4 / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.0904 Å
AuthorsMeyer, P.A. / Li, S. / Zhang, M. / Yamada, K. / Takagi, Y. / Hartzog, G.A. / Fu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100997 United States
CitationJournal: Mol.Cell.Biol. / Year: 2015
Title: Structures and Functions of the Multiple KOW Domains of Transcription Elongation Factor Spt5.
Authors: Meyer, P.A. / Li, S. / Zhang, M. / Yamada, K. / Takagi, Y. / Hartzog, G.A. / Fu, J.
History
DepositionMar 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 21, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.5Feb 28, 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

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Assembly

Deposited unit
A: Transcription elongation factor SPT5


Theoretical massNumber of molelcules
Total (without water)15,4241
Polymers15,4241
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.693, 44.394, 64.071
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 SPT5 / Chromatin elongation factor SPT5


Mass: 15423.502 Da / Num. of mol.: 1 / Fragment: UNP Residues 382-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SPT5, YML010W, YM9571.08 / Plasmid: pET24b(+) / Details (production host): pET24b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27692
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density meas: 1.36 Mg/m3 / Density % sol: 50 % / Description: bipyramids
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl, pH 8.0, 30% (w/v) PEG 3350 / PH range: 7.8 - 8.2 / Temp details: Forced air incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.5484, 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2013 / Details: 0.5 degree/image
RadiationMonochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54841
20.97931
ReflectionResolution: 1.09→36.5 Å / Num. all: 49082 / Num. obs: 48357 / % possible obs: 93.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/av σ(I): 14 / Net I/σ(I): 14
Reflection shellResolution: 1.09→1.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.6 / % possible all: 52.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000not knowndata reduction
HKL-2000not knowndata scaling
PHENIXnot knownphasing
RefinementMethod to determine structure: SAD
Starting model: experimental

Resolution: 1.0904→36.49 Å / Rfactor Rfree error: 0.01 / SU ML: 0.06 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 2478 5.12 %Random
Rwork0.1822 ---
obs0.1831 48357 93.91 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.318 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3436 Å2-0 Å20 Å2
2---0.4288 Å2-0 Å2
3---0.0853 Å2
Refinement stepCycle: LAST / Resolution: 1.0904→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 0 161 1104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009989
X-RAY DIFFRACTIONf_angle_d1.3211343
X-RAY DIFFRACTIONf_dihedral_angle_d13.272377
X-RAY DIFFRACTIONf_chiral_restr0.091145
X-RAY DIFFRACTIONf_plane_restr0.009176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0.01

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.0904-1.11140.24057150.23142453
1.1114-1.13410.23461220.1781182270
1.1341-1.15870.17381120.1644229485
1.1587-1.18570.16721360.1599257395
1.1857-1.21530.18681510.15242630100
1.2153-1.24820.15731300.14442693100
1.2482-1.28490.18771520.15062708100
1.2849-1.32640.16391490.15012665100
1.3264-1.37380.19311500.15262684100
1.3738-1.42880.17431460.15412703100
1.4288-1.49390.17921320.15062700100
1.4939-1.57260.17381550.15282700100
1.5726-1.67110.18781320.16362722100
1.6711-1.80020.18621570.17242713100
1.8002-1.98130.18171410.1722735100
1.9813-2.2680.20741420.18132765100
2.268-2.85720.22491460.2064277099
2.8572-36.51090.21561540.2176257889

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