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The cryo-EM structure of human TFIIH

by single particle reconstruction, at 4.4 A resolution

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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-3802, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 5of4
TitleThe cryo-EM structure of human TFIIH
DescriptorMAT1
Unassigned secondary structure elements.
(TFIIH basal transcription factor complex helicase ...) x 2
(General transcription factor IIH subunit ...) x 4
(Unassigned secondary structure elements ...) x 2
KeywordsTRANSCRIPTION, transcription initiation, DNA repair, multiprotein complex, kinase, helicase
AuthorsGreber, B.J., Nguyen, T.H.D., Fang, J., Afonine, P.V., Adams, P.D., Nogales, E.
DateDeposition: 2017-07-10, Release: 2017-09-13
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-3802, Imaged by UCSF CHIMERA

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EMDB-3802

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Article
Citation - primary
ArticleNature, Vol. 549, Issue 7672, Page 414-417, Year 2017
TitleThe cryo-electron microscopy structure of human transcription factor IIH.
AuthorsBasil J Greber, Thi Hoang Duong Nguyen, Jie Fang, Pavel V Afonine, Paul D Adams, Eva Nogales
California Institute for Quantitative Biology (QB3), University of California, Berkeley, California 94720, USA.
Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Miller Institute for Basic Research in Science, University of California, Berkeley, California 94720, USA.
Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.
Department of Bioengineering, University of California, Berkeley, California 94720, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.
LinksPubMed: 28902838, DOI: 10.1038/nature23903
Components
ID 1 : Basic transcription factor 2 89 kDa subunit,BTF2 p89,DNA excision repair protein ERCC-3,DNA repair protein complementing XP-B cells,TFIIH basal transcription factor complex 89 kDa subunit,TFIIH p89,Xeroderma pigmentosum group B-complementing protein,Basic transcription factor 2 89 kDa subunit,BTF2 p89,DNA excision repair protein ERCC-3,DNA repair protein complementing XP-B cells,TFIIH basal transcription factor complex 89 kDa subunit,TFIIH p89,Xeroderma pigmentosum group B-complementing protein
DescriptionTFIIH basal transcription factor complex helicase XPB subunit,XPB,TFIIH basal transcription factor complex helicase XPB subunit
Typepolypeptide(L)
Formula weight62426.047 Da
Number of molecules1
ID1
Ec3.6.4.12,3.6.4.12
SourceMethod: Isolated from a natural source
Src id: 2
Common name: Human
Alt source flag: sample
Beg seq num: 37
Cell line: HeLa
End seq num: 553
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: P19447, Sequence view
ID 2 : Basic transcription factor 2 80 kDa subunit,BTF2 p80,CXPD,DNA excision repair protein ERCC-2,DNA repair protein complementing XP-D cells,TFIIH basal transcription factor complex 80 kDa subunit,TFIIH p80,Xeroderma pigmentosum group D-complementing protein
DescriptionTFIIH basal transcription factor complex helicase XPD subunit
Typepolypeptide(L)
Formula weight87021.078 Da
Number of molecules1
ID2
Ec3.6.4.12
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
Cell line: HeLa
End seq num: 760
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: P18074, Sequence view
ID 3 : Basic transcription factor 2 52 kDa subunit,BTF2 p52,General transcription factor IIH polypeptide 4,TFIIH basal transcription factor complex p52 subunit,Basic transcription factor 2 52 kDa subunit,BTF2 p52,General transcription factor IIH polypeptide 4,TFIIH basal transcription factor complex p52 subunit
DescriptionGeneral transcription factor IIH subunit 4,p52,General transcription factor IIH subunit 4
Typepolypeptide(L)
Formula weight9875.401 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Src id: 2
Common name: Human
Alt source flag: sample
Beg seq num: 7
Cell line: HeLa
End seq num: 85
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q92759, Sequence view
ID 4 : Basic transcription factor 2 44 kDa subunit,BTF2 p44,General transcription factor IIH polypeptide 2,TFIIH basal transcription factor complex p44 subunit
DescriptionGeneral transcription factor IIH subunit 2
Typepolypeptide(L)
Formula weight44481.996 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
Cell line: HeLa
End seq num: 395
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q13888, Sequence view
ID 5 : Basic transcription factor 2 34 kDa subunit,BTF2 p34,General transcription factor IIH polypeptide 3,TFIIH basal transcription factor complex p34 subunit
DescriptionGeneral transcription factor IIH subunit 3
Typepolypeptide(L)
Formula weight34416.008 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
Cell line: HeLa
End seq num: 308
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q13889, Sequence view
ID 6 : General transcription factor IIH polypeptide 5,TFB5 ortholog,TFIIH basal transcription factor complex TTD-A subunit
DescriptionGeneral transcription factor IIH subunit 5
Typepolypeptide(L)
Formula weight8060.362 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
Cell line: HeLa
End seq num: 71
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: Q6ZYL4, Sequence view
ID 7 : MAT1
DescriptionMAT1
Typepolypeptide(L)
Formula weight10571.022 Da
Number of molecules1
ID7
DetailsSequence register unassigned.
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 124
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksSequence view
ID 8 : Unassigned secondary structure elements.
DescriptionUnassigned secondary structure elements.
Typepolypeptide(L)
Formula weight22996.232 Da
Number of molecules1
ID8
DetailsSequence unassigned.
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 270
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksSequence view
ID 9 : Unassigned secondary structure elements (p52 region)
DescriptionUnassigned secondary structure elements (p52 region)
Typepolypeptide(L)
Formula weight19762.281 Da
Number of molecules1
ID9
DetailsSequence unassigned
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 232
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksSequence view
ID 10 : Unassigned secondary structure elements (XPB NTE region)
DescriptionUnassigned secondary structure elements (XPB NTE region)
Typepolypeptide(L)
Formula weight6656.196 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 78
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksSequence view
ID 11 : IRON/SULFUR CLUSTER
DescriptionIRON/SULFUR CLUSTER
Typenon-polymer
Formula weight351.640 Da
Number of molecules1
ID11
SourceMethod: Obtained synthetically
Sample
Entity assembly
Entity id list1, 2, 3, 4, 5, 6, 7, 8, 9, 10
NameTFIIH
SourceNATURAL
TypeCOMPLEX
Entity assembly
Entity id list1, 2, 3, 4, 5, 6, 8, 9, 10
NameTFIIH core complex
Parent id1
SourceNATURAL
TypeCOMPLEX
Entity assembly
Entity id list7
NameTFIIH CDK-activating kinase (CAK) subcomplex
Parent id1
SourceNATURAL
TypeCOMPLEX
Buffer
Specimen id1
PH7.8
Experiment
Aggregation statePARTICLE
Reconstruction methodSINGLE PARTICLE
Sample support
Specimen id1
Grid materialCOPPER
Grid mesh size400
Grid typeC-flat-4/2
Vitrification
Specimen id1
Chamber temperature278.15
Cryogen nameETHANE
Details3-4 minute incubation, 2 second blot
Humidity100
InstrumentFEI VITROBOT MARK IV
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TITAN
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 37879 X
CsNominal: 2.7 mm
Nominal defocusMax: 4500 nm, Min: 2000 nm
Specimen holder
Specimen holderModel: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image scans
Image recording id1
Dimension height3710
Dimension width3840
Frames per image30
Sampling size5
Used frames per image1-30
Processing
Single particle entity
Image processing id1
Point symmetryC1
3D reconstruction
Image processing id1
AlgorithmFOURIER SPACE
DetailsRELION 3D auto-refinement (gold standard).
Num class averages3
Number of particles122900
Resolution4.4 A
Resolution methodFSC 0.143 CUT-OFF
Symmetry typePOINT
3D fitting
DetailsInitial model assembled from high-resolution structures and homology models. Subsequently rebuilt in O and COOT, refined into the cryo-EM map using PHENIX and REFMAC, and fully validated.
Refinement ProtocolRIGID BODY FIT
Refinement SpaceREAL
Refine
Refine id1
B iso mean193.578
Aniso B11-4.69
Aniso B12-0.80
Aniso B130.57
Aniso B22-3.42
Aniso B23-2.54
Aniso B338.11
Correlation coeff Fo to Fc0.939
DetailsHYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Ls R factor R work0.33528
Ls R factor obs0.33528
Ls d res high4.40 A
Ls d res low166.32 A
Ls number reflection obs82085
Ls percent reflection obs100.00
Overall SU B54.849
Overall SU ML0.668
Overall ESU R1.679
Solvent ion probe radii0.80
Solvent shrinkage radii0.80
Solvent vdw probe radii1.20
Stereochemistry target valuesMAXIMUM LIKELIHOOD WITH PHASES
Solvent model detailsMASK
Refine
Refine idELECTRON MICROSCOPY
Refine hist
Cycle id1
Refine idELECTRON MICROSCOPY
Total atoms17200
Software
Ordinal1
Classificationrefinement
NameREFMAC
Version5.8.0158
Download
PDB format
Allpdb5of4.ent.gz
pdb5of4.ent (uncompressed file)
Header onlypdb5of4.ent.gz
mmCIF format
mmCIF5of4.cif.gz
XML format
All5of4.xml.gz
No-atom5of4-noatom.xml.gz
Ext-atom5of4-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 5.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 6.2 MB