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- PDB-6mzm: Human TFIID bound to promoter DNA and TFIIA -

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Basic information

Entry
Database: PDB / ID: 6mzm
TitleHuman TFIID bound to promoter DNA and TFIIA
Components
  • (SCP DNA (80-MER)) x 2
  • (Transcription initiation factor IIA subunit ...) x 2
  • (Transcription initiation factor TFIID subunit ...) x 11
  • TATA-box-binding protein
  • Unk
Keywordstranscription/dna / Transcription / DNA / Nuclear / transcription-dna complex
Function / homologyPeptidase M1 N-terminal domain / Transcription initiation factor TFIID subunit 8 / TATA-box binding protein, eukaryotic / WD40-repeat-containing domain superfamily / TAFH/NHR1 domain superfamily / TFIID subunit TAF5, NTD2 domain superfamily / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 2 ...Peptidase M1 N-terminal domain / Transcription initiation factor TFIID subunit 8 / TATA-box binding protein, eukaryotic / WD40-repeat-containing domain superfamily / TAFH/NHR1 domain superfamily / TFIID subunit TAF5, NTD2 domain superfamily / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 7 / Transcription factor TFIID (or TATA-binding protein, TBP) / G-protein beta WD-40 repeat / WD domain, G-beta repeat / Transcription initiation factor IIA, gamma subunit, helical domain / TATA-box binding protein / Transcription initiation factor IIA, gamma subunit / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID subunit A / WD40 associated region in TFIID subunit, NTD2 domain / TAFII55 protein conserved region / TATA-box binding protein, conserved site / WD40 repeat, conserved site / Bromodomain associated / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TAFII31 / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor TFIID subunit 12 domain / TAFH/NHR1 / Transcription initiation factor TFIID, 23-30kDa subunit / TATA box binding protein associated factor (TAF) / Bromodomain associated domain / LIS1 homology motif / TAFII55 protein, conserved region / Transcription initiation factor TFIID component TAF4 / Transcription factor TFIID, subunit 8, C-terminal / Histone-fold / Transcription factor IIA, helical / Transcription factor IIA, beta-barrel / TAF6, C-terminal HEAT repeat domain / TBP domain superfamily / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / WD40-repeat-containing domain / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor IID, 31kD subunit / NHR1 homology to TAF / RNA Polymerase I Chain Elongation / Ub-specific processing proteases / RNA Polymerase II Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / TAF6 C-terminal HEAT repeat domain / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / NoRC negatively regulates rRNA expression / RNA Polymerase I Transcription Termination / RNA Polymerase III Abortive And Retractive Initiation / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Estrogen-dependent gene expression / B-WICH complex positively regulates rRNA expression / RNA Polymerase II Promoter Escape / WD40 repeat / Transcription factor TFIID repeat signature. / TAFH/NHR1 domain profile. / HIV Transcription Initiation / SIRT1 negatively regulates rRNA expression / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats signature. / RNA Polymerase II HIV Promoter Escape / Trp-Asp (WD) repeats circular profile. / Transcription of the HIV genome / HATs acetylate histones / Transcription factor TFIID complex subunit 8 C-term / LIS1 homology (LisH) motif profile. / spermine transport / P-TEFb complex binding / regulation of transcription initiation from RNA polymerase II promoter / pre-snoRNP complex / STAGA complex / transcription factor TFTC complex / RNA polymerase II general transcription initiation factor activity / inner cell mass cell proliferation / PCAF complex / SLIK (SAGA-like) complex / TFIIH-class transcription factor complex binding / regulation of DNA binding / maintenance of protein location in nucleus / SAGA complex / transcription factor TFIIIB complex / transcription factor TFIIA complex / RNA polymerase III general transcription initiation factor activity
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.5 Å resolution
AuthorsPatel, A.B. / Louder, R.K. / Greber, B.J. / Grunberg, S. / Luo, J. / Fang, J. / Liu, Y. / Ranish, J. / Hahn, S. / Nogales, E.
CitationJournal: Science / Year: 2018
Title: Structure of human TFIID and mechanism of TBP loading onto promoter DNA.
Authors: Avinash B Patel / Robert K Louder / Basil J Greber / Sebastian Grünberg / Jie Luo / Jie Fang / Yutong Liu / Jeff Ranish / Steve Hahn / Eva Nogales
Abstract: The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and ...The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and initiating PIC assembly. We used cryo-electron microscopy (cryo-EM), chemical crosslinking-mass spectrometry (CX-MS) and biochemical reconstitution to determine the complete molecular architecture of TFIID and define the conformational landscape of TFIID in the process of TATA-box binding protein (TBP) loading onto promoter DNA. Our structural analysis revealed five structural states of TFIID in the presence of TFIIA and promoter DNA, showing that the initial binding of TFIID to the downstream promoter positions the upstream DNA and facilitates scanning of TBP for a TATA-box and the subsequent engagement of the promoter. Our findings provide a mechanistic model for the specific loading of TBP by TFIID onto the promoter.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 5, 2018 / Release: Nov 28, 2018

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 1, TAF1
B: Transcription initiation factor TFIID subunit 2, TAF2
D: Transcription initiation factor TFIID subunit 4, TAF4
G: Transcription initiation factor TFIID subunit 5,TAF5
H: Transcription initiation factor TFIID subunit 6
I: Transcription initiation factor TFIID subunit 6
J: Transcription initiation factor TFIID subunit 7
K: Transcription initiation factor TFIID subunit 8, TAF8
L: Transcription initiation factor TFIID subunit 9, TAF9
O: Transcription initiation factor TFIID subunit 10
R: Transcription initiation factor TFIID subunit 12
T: TATA-box-binding protein
U: SCP DNA (80-MER)
V: SCP DNA (80-MER)
W: Transcription initiation factor IIA subunit 1
X: Transcription initiation factor IIA subunit 2
Z: Unk


Theoretical massNumber of molelcules
Total (without water)800,42417
Polyers800,42417
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Transcription initiation factor TFIID subunit ... , 11 types, 11 molecules ABDGHIJKLOR

#1: Protein/peptide Transcription initiation factor TFIID subunit 1, TAF1


Mass: 57193.742 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#2: Protein/peptide Transcription initiation factor TFIID subunit 2, TAF2 / 150 kDa cofactor of initiator function


Mass: 137159.984 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P1X5
#3: Protein/peptide Transcription initiation factor TFIID subunit 4, TAF4


Mass: 104052.086 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O00268
#4: Protein/peptide Transcription initiation factor TFIID subunit 5,TAF5 / Transcription initiation factor TFIID 100 kDa subunit / TAFII100


Mass: 85785.164 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15542
#5: Protein/peptide Transcription initiation factor TFIID subunit 6 / RNA polymerase II TBP-associated factor subunit E


Mass: 72749.297 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P49848
#6: Protein/peptide Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID 70 kDa subunit


Mass: 72365.836 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P49848
#7: Protein/peptide Transcription initiation factor TFIID subunit 7 / RNA polymerase II TBP-associated factor subunit F / Transcription initiation factor TFIID 55 kDa subunit / TAFII55


Mass: 40325.117 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15545
#8: Protein/peptide Transcription initiation factor TFIID subunit 8, TAF8 / Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8 / Transcription initiation factor TFIID 43 kDa subunit / hTAFII43 / Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8


Mass: 32975.344 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7C8
#9: Protein/peptide Transcription initiation factor TFIID subunit 9, TAF9 / RNA polymerase II TBP-associated factor subunit G / STAF31/32 / Transcription initiation factor TFIID 31 kDa subunit / TAFII31 / Transcription initiation factor TFIID 32 kDa subunit / TAFII32


Mass: 28830.689 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q16594
#10: Protein/peptide Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAFII30


Mass: 21731.248 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q12962
#11: Protein/peptide Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID 20/15 kDa subunits / TAFII20/TAFII15


Mass: 17948.467 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q16514

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Protein/peptide , 2 types, 2 molecules TZ

#12: Protein/peptide TATA-box-binding protein / TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation factor TFIID TBP subunit


Mass: 37729.938 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P20226
#17: Protein/peptide Unk


Mass: 20272.906 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)

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DNA chain , 2 types, 2 molecules UV

#13: DNA chain SCP DNA (80-MER)


Mass: 24498.586 Da / Num. of mol.: 1 / Source: (synth.) Homo sapiens (human)
#14: DNA chain SCP DNA (80-MER)


Mass: 24854.842 Da / Num. of mol.: 1 / Source: (synth.) Homo sapiens (human)

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Transcription initiation factor IIA subunit ... , 2 types, 2 molecules WX

#15: Protein/peptide Transcription initiation factor IIA subunit 1 / General transcription factor IIA subunit 1 / TFIIAL / Transcription initiation factor TFIIA 42 kDa subunit / TFIIA-42


Mass: 10675.194 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A1, TF2A1 / Production host: Escherichia coli (E. coli)
#16: Protein/peptide Transcription initiation factor IIA subunit 2 / General transcription factor IIA subunit 2 / TFIIA p12 subunit / TFIIAS / Transcription initiation factor IIA gamma chain / TFIIA-gamma


Mass: 11275.824 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A2, TF2A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52657

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: General transcription factor IID / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17
Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa
Buffer solutionpH: 7.9
Buffer component
IDConc.FormulaBuffer ID
110 mMHEPES1
210 mMMgCl1
31 mMDTT1
43 %Trehalose1
550 mMKCl1
6.0125 %NP-401
SpecimenConc.: .2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins / Details: BT 4s; BF 15N

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 50 microns
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3211: / Classification: refinement
EM software
IDNameCategory
2Leginonimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 25180 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00433220
ELECTRON MICROSCOPYf_angle_d0.91845740
ELECTRON MICROSCOPYf_dihedral_angle_d12.30719501
ELECTRON MICROSCOPYf_chiral_restr0.0535250
ELECTRON MICROSCOPYf_plane_restr0.0075318

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