[English] 日本語
Yorodumi
- PDB-2exu: Crystal Structure of Saccharomyces cerevisiae transcription elong... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2exu
TitleCrystal Structure of Saccharomyces cerevisiae transcription elongation factors Spt4-Spt5NGN domain
ComponentsTranscription initiation protein SPT4/SPT5
KeywordsTRANSCRIPTION / helixs surrounding beta sheet
Function / homology
Function and homology information


negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / mating-type region heterochromatin / regulation of transcription-coupled nucleotide-excision repair / regulation of rRNA processing / RNA polymerase I core binding / intracellular mRNA localization / DSIF complex / rDNA heterochromatin / RNA polymerase I general transcription initiation factor binding ...negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / mating-type region heterochromatin / regulation of transcription-coupled nucleotide-excision repair / regulation of rRNA processing / RNA polymerase I core binding / intracellular mRNA localization / DSIF complex / rDNA heterochromatin / RNA polymerase I general transcription initiation factor binding / rDNA binding / U4 snRNA binding / snRNP binding / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation-coupled chromatin remodeling / RNA Polymerase II Pre-transcription Events / spliceosomal complex assembly / RNA polymerase II complex binding / 7-methylguanosine mRNA capping / U5 snRNA binding / U2 snRNA binding / U6 snRNA binding / U1 snRNA binding / positive regulation of autophagy / negative regulation of autophagy / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / kinetochore / heterochromatin formation / chromatin organization / histone binding / rRNA binding / chromatin remodeling / mRNA binding / regulation of DNA-templated transcription / protein-containing complex binding / chromatin / 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 / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain ...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 / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, fourth KOW domain / 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 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / 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 / 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
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_struct_conn_angle / software / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein Transcription initiation protein SPT4/SPT5


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


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


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
REFMAC5refinement
PDB_EXTRACT1.7data extraction
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more