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- PDB-4ytl: Structure of the KOW2-KOW3 Domain of Transcription Elongation Fac... -

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Basic information

Entry
Database: PDB / ID: 4ytl
TitleStructure of the KOW2-KOW3 Domain of Transcription Elongation Factor Spt5.
ComponentsTranscription elongation factor SPT5
KeywordsTRANSCRIPTION / Spt5 / RNA processing / Transcription elongation.
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 / snRNP binding / regulation of rRNA processing / intracellular mRNA localization / RNA polymerase I core binding / DSIF complex / 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 / snRNP binding / regulation of rRNA processing / intracellular mRNA localization / RNA polymerase I core binding / DSIF complex / 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 / spliceosomal complex assembly / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / 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 / SH3 type barrels. - #30 / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / SH3 type barrels. / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW / KOW motif / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
Transcription elongation factor SPT5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.601 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

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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)22,4368
Polymers21,8682
Non-polymers5686
Water4,342241
1
A: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0302
Polymers10,9341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4066
Polymers10,9341
Non-polymers4725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.253, 54.243, 95.153
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: 10934.025 Da / Num. of mol.: 2
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(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27692
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.5 Å3/Da / Density meas: 1.36 Mg/m3 / Density % sol: 52.9 % / Description: Rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium citrate (pH 5.0), 0.5 M ammonium sulfate, and 1.0 M lithium sulfate
PH range: 4.8 - 5.2

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: rotation step: 0.5 degree
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2013 / Details: rotation: 0.5 degree
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 28098 / Num. obs: 27657 / % possible obs: 89.5 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 82.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 12.1 / % possible all: 52.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.601→35.768 Å / Rfactor Rfree error: 0.01 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 1391 5.03 %Random
Rwork0.1851 ---
obs0.186 27657 89.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.601→35.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 32 241 1764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191555
X-RAY DIFFRACTIONf_angle_d1.6552109
X-RAY DIFFRACTIONf_dihedral_angle_d13.305571
X-RAY DIFFRACTIONf_chiral_restr0.135252
X-RAY DIFFRACTIONf_plane_restr0.01272
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6008-1.6580.2512980.1833158956
1.658-1.72440.21471050.19192467
1.7244-1.80290.23561190.1864230379
1.8029-1.89790.21371330.1921265391
1.8979-2.01680.19741490.17422919100
2.0168-2.17260.17981680.17162892100
2.1726-2.39110.21351770.18512903100
2.3911-2.7370.22241340.19912976100
2.737-3.44790.2131480.19722988100
3.4479-35.77660.18021600.17633119100
Refinement TLS params.Method: refined / Origin x: 12.1492 Å / Origin y: 61.7235 Å / Origin z: 11.3888 Å
111213212223313233
T0.0439 Å2-0.0008 Å2-0.003 Å2-0.0491 Å20.0064 Å2--0.0355 Å2
L0.6052 °20.1434 °2-0.1668 °2-0.5192 °2-0.2075 °2--0.479 °2
S0.0231 Å °-0.0722 Å °-0.0383 Å °0.0134 Å °-0.0307 Å °-0.0109 Å °-0.0123 Å °0.0364 Å °-0.0085 Å °
Refinement TLS groupSelection details: all

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