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- PDB-2exu: Crystal Structure of Saccharomyces cerevisiae transcription elong... -

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Basic information

Entry
Database: PDB / ID: 2exu
TitleCrystal Structure of Saccharomyces cerevisiae transcription elongation factors Spt4-Spt5NGN domain
ComponentsTranscription initiation protein SPT4/SPT5Transcription (biology)
KeywordsTRANSCRIPTION / helixs surrounding beta sheet
Function / homology
Function and homology information


RNA Polymerase II Transcription Elongation / negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / heterochromatin formation => GO:0031507 / 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 II Transcription Elongation / negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / heterochromatin formation => GO:0031507 / regulation of transcription-coupled nucleotide-excision repair / snRNP binding / regulation of rRNA processing / intracellular mRNA localization / RNA polymerase I core binding / DSIF complex / regulation of transcription elongation by RNA polymerase II / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / 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 / 7-methylguanosine mRNA capping / U5 snRNA binding / U2 snRNA binding / U6 snRNA binding / positive regulation of autophagy / U1 snRNA binding / negative regulation of autophagy / chromosome segregation / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / mRNA splicing, via spliceosome / kinetochore / mRNA processing / chromosome / chromatin organization / rRNA binding / mRNA binding / protein-containing complex binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Herpes Virus-1 - #210 / NusG, N-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / 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 C-terminal nonapeptide repeat binding Spt4 / 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
ETHANOL / Transcription elongation factor SPT5 / Transcription elongation factor SPT4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.23 Å
AuthorsXu, F. / Guo, M. / Fang, P. / Teng, M. / Niu, L.
CitationJournal: To be published
Title: Crystal Structure of Saccharomyces cerevisiae transcription elongation factors Spt4-Spt5NGN domain
Authors: Xu, F. / Guo, M. / Fang, P. / Teng, M. / Niu, L.
History
DepositionNov 8, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription initiation protein SPT4/SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9005
Polymers22,6251
Non-polymers2764
Water1,982110
1
A: Transcription initiation protein SPT4/SPT5
hetero molecules

A: Transcription initiation protein SPT4/SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,80010
Polymers45,2492
Non-polymers5518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z+3/41
Buried area7020 Å2
ΔGint-49 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.801, 53.801, 177.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsThe biological assembly is a heterodimer containing a Spt4(Entity 1) and a Spt5 NGN domain (Entity 2) generated by the operation: y, x, -z

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Components

#1: Protein Transcription initiation protein SPT4/SPT5 / Transcription (biology)


Mass: 22624.502 Da / Num. of mol.: 1 / Fragment: Spt4, Spt5 NGN domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPT4, SPT5 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P32914, UniProt: P27692
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 30% EtOH, 50mM NaCl, 100mM Tris-HCl, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONBSRF 3W1A11.2834
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMay 3, 2005
MARRESEARCH2CCDApr 26, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.28341
21.54181
ReflectionRedundancy: 6 % / Number: 5315 / Rmerge(I) obs: 0.058 / Χ2: 1.139 / D res high: 3.03 Å / D res low: 20 Å / % possible obs: 95.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.462096.710.0461.6695.3
5.166.4698.110.0551.5055.9
4.515.1698.210.0511.2546
4.114.5197.510.0511.156
3.814.1197.410.0521.1286.2
3.593.8197.410.0590.996.2
3.413.5997.810.0610.966.2
3.263.4196.910.0740.956.2
3.143.2696.810.0880.8246.3
3.033.1477.510.1160.8895.3
ReflectionResolution: 2.22→53.84 Å / Num. all: 13617 / Num. obs: 13576 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 5.4
Reflection shellResolution: 2.23→2.33 Å / % possible obs: 97.6 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.8 / Num. measured obs: 1627 / Rsym value: 0.262 / % possible all: 99.7

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Phasing

PhasingMethod: SAD
Phasing MAD set siteAtom type symbol: Zn / B iso: 36.922 / Fract x: 0.228 / Fract y: 0.096 / Fract z: 0.078 / Occupancy: 1.062
Phasing dmFOM : 0.73 / FOM acentric: 0.74 / FOM centric: 0.68 / Reflection: 13500 / Reflection acentric: 10780 / Reflection centric: 2720
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.4-21.4240.890.940.81660363297
4-6.40.90.930.8318851356529
3.2-40.850.850.8222681793475
2.8-3.20.780.810.6822841859425
2.4-2.80.660.680.5539783342636
2.2-2.40.530.550.4224252067358

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
MARdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.23→21.42 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.729 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.237 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.221 686 5.1 %RANDOM
Rwork0.206 ---
all0.207 13617 --
obs0.207 13499 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.784 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2--0.75 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.23→21.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 15 110 1628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221543
X-RAY DIFFRACTIONr_angle_refined_deg0.9941.9962074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9175190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72623.89859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31115294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0661510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021114
X-RAY DIFFRACTIONr_nbd_refined0.1810.2711
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21056
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.226
X-RAY DIFFRACTIONr_mcbond_it0.2491.5988
X-RAY DIFFRACTIONr_mcangle_it0.42521546
X-RAY DIFFRACTIONr_scbond_it0.7233630
X-RAY DIFFRACTIONr_scangle_it1.1684.5528
LS refinement shellResolution: 2.225→2.344 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.259 95 -
Rwork0.217 1769 -
all-1864 -
obs--100 %
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)
12.94770.7152-1.3641.9218-1.12693.6578-0.03240.08090.0767-0.28760.0089-0.0355-0.0428-0.10840.0234-0.1008-0.0072-0.0161-0.17510.0002-0.121646.559.236858.3463
22.7735-0.55321.19837.0502-0.39858.67320.04150.04080.0161-0.17420.02560.01670.3467-0.0045-0.0671-0.054-0.0075-0.0492-0.19830.0162-0.123957.987-20.556458.7174
30.14010.0041-0.12971.3354-0.2670.3790.00420.0212-0.0119-0.14560.00660.01150.0592-0.0207-0.01080.1159-0.0116-0.0140.06560.0240.033551.7714-3.249159.7281
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A3 - 1013 - 101
21D10021
31E20011
42A285 - 377102 - 194
52C10011
63F2002 - 21111 - 110

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