[English] 日本語
Yorodumi
- PDB-1h3o: Crystal Structure of the Human TAF4-TAF12 (TAFII135-TAFII20) Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h3o
TitleCrystal Structure of the Human TAF4-TAF12 (TAFII135-TAFII20) Complex
Components
  • TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT
  • TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS
KeywordsTRANSCRIPTION/TBP-ASSOCIATED FACTORS / TBP-ASSOCIATED FACTORS / TFIID / RNA POLYMERASE II TRANSCRIPTION / HISTONE FOLD DOMAINS / NUCLEAR PROTEIN / TRANSCRIPTION-TBP-ASSOCIATED FACTORS complex
Function / homology
Function and homology information


transcription factor TFTC complex / SLIK (SAGA-like) complex / SAGA complex / transcription factor TFIID complex / regulation of RNA splicing / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...transcription factor TFTC complex / SLIK (SAGA-like) complex / SAGA complex / transcription factor TFIID complex / regulation of RNA splicing / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / MLL1 complex / aryl hydrocarbon receptor binding / positive regulation of transcription initiation by RNA polymerase II / regulation of DNA repair / ovarian follicle development / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / male germ cell nucleus / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / HATs acetylate histones / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / protein heterodimerization activity / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Transcription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A ...Transcription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / Transcription initiation factor TFIID subunit 12 domain / Histone, subunit A / Histone, subunit A / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 4 / Transcription initiation factor TFIID subunit 12
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsWerten, S. / Mitschler, A. / Moras, D.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of a Subcomplex of Human Transcription Factor TFIID Formed by TATA Binding Protein-Associated Factors Htaf4 (Htaf(II)135) and Htaf12 (Htaf(II)20).
Authors: Werten, S. / Mitschler, A. / Romier, C. / Gangloff, Y.-G. / Thuault, S. / Davidson, I. / Moras, D.
#1: Journal: Mol.Cell.Biol. / Year: 2000
Title: The Human TFIID Components Tafii135 and Tafii20 and the Yeast Saga Components Ada1 and Tafii68 Heterodimerize to Form Histone-Like Pairs
Authors: Gangloff, Y.-G. / Werten, S. / Romier, C. / Carre, L. / Poch, O. / Moras, D. / Davidson, I.
History
DepositionSep 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT
B: TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS
C: TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT
D: TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS


Theoretical massNumber of molelcules
Total (without water)35,7354
Polymers35,7354
Non-polymers00
Water2,846158
1
A: TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT
B: TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS


Theoretical massNumber of molelcules
Total (without water)17,8682
Polymers17,8682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT
D: TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS


Theoretical massNumber of molelcules
Total (without water)17,8682
Polymers17,8682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)112.940, 36.825, 73.948
Angle α, β, γ (deg.)90.00, 97.85, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.96526, -0.00695, 0.26119), (-0.0106, -0.99986, 0.01257), (0.26106, -0.0149, -0.96521)
Vector: -13.50713, 27.68045, 102.79547)
DetailsTWO HETERODIMERS FORMED BY CHAINS A AND B , OR CHAINSC AND D.

-
Components

#1: Protein TRANSCRIPTION INITIATION FACTOR TFIID 135 KDA SUBUNIT / TAFII-135 / TAFII135 / TAFII-130 / TAFII130 / TAF4A / TAF2C / HTAF4


Mass: 8813.803 Da / Num. of mol.: 2 / Fragment: HISTONE FOLD DOMAIN, RESIDUES 870-943 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL SELENOMETHIONINE INSERT, UNIFORM SELENO-METHIONINE LABELING
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Plasmid: PACYC-11B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00268
#2: Protein TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS / TAFII-20/TAFII-15 / TAFII20/TAFII15 / TAF12 / TAF2J


Mass: 9053.836 Da / Num. of mol.: 2 / Fragment: HISTONE FOLD DOMAIN, RESIDUES 57-128 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES (GLY SER HIS MSE) INSERTED AT THE N-TERMINUS, REMAINDER OF HISTIDINE-TAG AFTER THROMBIN TREATMENT, UNIFORM SELENO-METHIONINE LABELING
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16514
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHTAF4: MULTIMERIC PROTEIN COMPLEX THAT PLAYS A CENTRAL ROLE IN MEDIATING PROMOTER RESPONSES TO ...HTAF4: MULTIMERIC PROTEIN COMPLEX THAT PLAYS A CENTRAL ROLE IN MEDIATING PROMOTER RESPONSES TO VARIOUS ACTIVATORS AND REPRESSORS. HTAF12: BELONGS TO THE TAF2J FAMILY. MAKES INTERACTIONS WITH TBP. TWO ISOFORMS PRODUCED BY ALTERNATIVE INITIATION. HTAF4: CONTAINS A SELENOMETHIONINE INSERTION AT N-TERMINUS MSE 869 CHAINS A AND C. HTAF12: CONTAINS A 4 RESIDUE INSERTION (GLY SER HIS MSE) AT N-TERMINUS RESIDUES 53-56 CHAINS B AND D.
Sequence detailsENGINEERED DELETION MUTANT THE HTAF12 POLYPEPTIDE THAT WAS USED FOR CRYSTALLIZATION CONTAINED THE ...ENGINEERED DELETION MUTANT THE HTAF12 POLYPEPTIDE THAT WAS USED FOR CRYSTALLIZATION CONTAINED THE SEQUENCE GLY-SER-HIS-MET (ORIGINATING FROM THE EXPRESSION PLASMID) AT ITS N TERMINUS. NO ELECTRON DENSITY WAS SEEN FOR THE FIRST TWO OF THESE RESIDUES (GLY-SER, NOT PRESENT IN THE MODEL), WHEREAS THE THIRD (HIS) HAS BEEN REPLACED BY ALA IN THE MODEL (NO DENSITY WAS SEEN FOR ITS SIDE CHAIN).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 42 %
Description: DATA QUALITY STATISTICS LISTED PERTAIN TO REMOTE WAVELENGTH DATA (0.90730 A)
Crystal growpH: 5.25 / Details: pH 5.25
Crystal grow
*PLUS
Temperature: 24 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mMdithiothreitol1drop
210-15 mg/mlprotein1drop
3100 mMsodium acetate1reservoirpH5.25
42.2 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.90730,0.97740
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 9, 2001 / Details: PREMIRROR, BENT MIRROR
RadiationMonochromator: DOUBLE CRYSTAL FOCUSSING MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.90731
20.97741
ReflectionResolution: 2.3→20 Å / Num. obs: 24237 / % possible obs: 92.3 % / Redundancy: 1.5 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.034 / Net I/σ(I): 19.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 4.45 / Rsym value: 0.167 / % possible all: 90.1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 25898 / % possible obs: 98.9 % / Num. measured all: 61754 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 2588 / Num. measured obs: 6073 / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 7.56

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→19.63 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1965882.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: NO ELECTRON DENSITY WAS OBSERVED FOR THE C-TERMINAL PORTION OF HTAF4, RESIDUES 918-943, WHICH IS THEREFORE ABSENT FROM THE MODEL. THE FACT THAT PART OF THE PROTEIN COMPLEX DID NOT SHOW UP IN ...Details: NO ELECTRON DENSITY WAS OBSERVED FOR THE C-TERMINAL PORTION OF HTAF4, RESIDUES 918-943, WHICH IS THEREFORE ABSENT FROM THE MODEL. THE FACT THAT PART OF THE PROTEIN COMPLEX DID NOT SHOW UP IN ELECTRON DENSITY MAPS WAS NOT DUE TO PROTEOLYSIS (AS EVIDENCED BY MASS SPECTROSCOPY OF REDISSOLVED CRYSTALS), INDICATING THAT THE REGIONS INVOLVED ARE DISORDERED WITHIN THE CRYSTAL LATTICE.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 646 5.1 %RANDOM
Rwork0.226 ---
obs0.226 12646 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.9338 Å2 / ksol: 0.357292 e/Å3
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.44 Å20 Å20.3 Å2
2--20.01 Å20 Å2
3----15.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 0 158 2172
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it2.492
X-RAY DIFFRACTIONc_scangle_it3.712.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 91 5 %
Rwork0.259 1746 -
obs--82 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69

+
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