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- EMDB-0452: Cryo-EM structure of the human TFIIH core complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0452
TitleCryo-EM structure of the human TFIIH core complex
Map dataSharpened and low-pass filtered cryo-EM map.
Sample
  • Complex: Transcription factor IIH (TFIIH)
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPB
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPD
    • Protein or peptide: General transcription factor IIH subunit 1, p62
    • Protein or peptide: General transcription factor IIH subunit 4, p52
    • Protein or peptide: General transcription factor IIH subunit 2, p44
    • Protein or peptide: General transcription factor IIH subunit 3, p34
    • Protein or peptide: General transcription factor IIH subunit 5, p8
    • Protein or peptide: CDK-activating kinase assembly factor MAT1
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ZINC ION
Keywordstranscription / DNA repair / helicase / multiprotein complex
Function / homology
Function and homology information


MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / ventricular system development / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / ventricular system development / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / CAK-ERCC2 complex / transcription factor TFIIK complex / UV protection / embryonic cleavage / DNA 5'-3' helicase / G protein-coupled receptor internalization / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / nuclear thyroid hormone receptor binding / regulation of cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase I Transcription Termination / transcription preinitiation complex / regulation of mitotic cell cycle phase transition / 3'-5' DNA helicase activity / DNA 3'-5' helicase / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / spinal cord development / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / hematopoietic stem cell proliferation / erythrocyte maturation / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / bone mineralization / 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 / regulation of G1/S transition of mitotic cell cycle / ATPase activator activity / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / RNA Polymerase I Transcription Initiation / hematopoietic stem cell differentiation / embryonic organ development / Tat-mediated elongation of the HIV-1 transcript / transcription by RNA polymerase I / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription elongation by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / Cyclin E associated events during G1/S transition / DNA helicase activity / Cyclin A/B1/B2 associated events during G2/M transition / response to UV / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Transcription Elongation / cyclin-dependent protein kinase holoenzyme complex / Formation of RNA Pol II elongation complex / hormone-mediated signaling pathway / RNA Polymerase II Pre-transcription Events / extracellular matrix organization / insulin-like growth factor receptor signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-embryonic development / determination of adult lifespan / isomerase activity / nucleotide-excision repair / chromosome segregation / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II / positive regulation of smooth muscle cell proliferation / promoter-specific chromatin binding / cellular response to gamma radiation / NoRC negatively regulates rRNA expression / multicellular organism growth / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / spindle / G1/S transition of mitotic cell cycle / Formation of Incision Complex in GG-NER / response to calcium ion / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / protein localization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / double-stranded DNA binding
Similarity search - Function
TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 ...TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Helical and beta-bridge domain / Helical and beta-bridge domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / ATP-dependent helicase Rad3/Chl1-like / : / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / C1-like domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / von Willebrand factor A-like domain superfamily / Ring finger / Zinc finger C2H2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / helicase superfamily c-terminal domain / PH-like domain superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / General transcription factor IIH subunit 1 / CDK-activating kinase assembly factor MAT1 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGreber BJ / Toso D
Funding support United States, Switzerland, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM63072 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM063210 United States
Swiss National Science FoundationP300PA_160983 Switzerland
Swiss National Science FoundationP300PA_174355 Switzerland
CitationJournal: Elife / Year: 2019
Title: The complete structure of the human TFIIH core complex.
Authors: Basil J Greber / Daniel B Toso / Jie Fang / Eva Nogales /
Abstract: Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is ...Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations.
History
DepositionJan 10, 2019-
Header (metadata) releaseFeb 13, 2019-
Map releaseMar 13, 2019-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0172
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0172
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nmi
  • Surface level: 0.0172
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0452.png

Downloads & links

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Map

FileDownload / File: emd_0452.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened and low-pass filtered cryo-EM map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0172 / Movie #1: 0.0172
Minimum - Maximum-0.069341935 - 0.14785278
Average (Standard dev.)0.0001731863 (±0.003722968)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z294.400294.400294.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0690.1480.000

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Supplemental data

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Half map: Unfiltered half-map.

Fileemd_0452_half_map_1.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map.

Fileemd_0452_half_map_2.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transcription factor IIH (TFIIH)

EntireName: Transcription factor IIH (TFIIH)
Components
  • Complex: Transcription factor IIH (TFIIH)
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPB
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPD
    • Protein or peptide: General transcription factor IIH subunit 1, p62
    • Protein or peptide: General transcription factor IIH subunit 4, p52
    • Protein or peptide: General transcription factor IIH subunit 2, p44
    • Protein or peptide: General transcription factor IIH subunit 3, p34
    • Protein or peptide: General transcription factor IIH subunit 5, p8
    • Protein or peptide: CDK-activating kinase assembly factor MAT1
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ZINC ION

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Supramolecule #1: Transcription factor IIH (TFIIH)

SupramoleculeName: Transcription factor IIH (TFIIH) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: General transcription and DNA repair factor IIH helicase subunit XPB

MacromoleculeName: General transcription and DNA repair factor IIH helicase subunit XPB
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.233492 KDa
SequenceString: PQEAVPSAAG KQVDESGTKV DEYGAKDYRL QMPLKDDHTS RPLWVAPDGH IFLEAFSPVY KYAQDFLVAI AEPVCRPTHV HEYKLTAYS LYAAVSVGLQ TSDITEYLRK LSKTGVPDGI MQFIKLCTVS YGKVKLVLKH NRYFVESCHP DVIQHLLQDP V IRECRLRN ...String:
PQEAVPSAAG KQVDESGTKV DEYGAKDYRL QMPLKDDHTS RPLWVAPDGH IFLEAFSPVY KYAQDFLVAI AEPVCRPTHV HEYKLTAYS LYAAVSVGLQ TSDITEYLRK LSKTGVPDGI MQFIKLCTVS YGKVKLVLKH NRYFVESCHP DVIQHLLQDP V IRECRLRN SE(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)QTVSFEVKQ EMIEELQKRC IHLEYPLLAE YDFRNDSVNP DINIDLKPTA VLRPYQEKSL R KMFGNGRA RSGVIVLPCG AGKSLVGVTA ACTVRKRCLV LGNSAVSVEQ WKAQFKMWST IDDSQICRFT SDAKDKPIGC SV AISTYSM LGHTTKRSWE AERVMEWLKT QEWGLMILDE VHTIPAKMFR RVLTIVQAHC KLGLTATLVR EDDKIVDLNF LIG PKLYEA NWMELQNNGY IAKVQCAEVW CPMSPEFYRE YVAIKTKKRI LLYTMNPNKF RACQFLIKFH ERRNDKIIVF ADNV FALKE YAIRLNKPYI YGPTSQGERM QILQNFKHNP KINTIFISKV GDTSFDLPEA NVLIQISSHG GSRRQEAQRL GRVLR AKKG MVAEEYNAFF YSLVSQDTQE MAYSTKRQRF LVDQGYSFKV ITKLAGMEEE DLAFSTKEEQ QQLLQKVLAA TDLDAE EEV VA

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Macromolecule #2: General transcription and DNA repair factor IIH helicase subunit XPD

MacromoleculeName: General transcription and DNA repair factor IIH helicase subunit XPD
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.417766 KDa
SequenceString: MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ RAYPLEVTKL IYCSRTVPEI EKVIEELRK LLNFYEKQEG EKLPFLGLAL SSRKNLCIHP EVTPLRFGKD VDGKCHSLTA SYVRAQYQHD TSLPHCRFYE E FDAHGREV ...String:
MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ RAYPLEVTKL IYCSRTVPEI EKVIEELRK LLNFYEKQEG EKLPFLGLAL SSRKNLCIHP EVTPLRFGKD VDGKCHSLTA SYVRAQYQHD TSLPHCRFYE E FDAHGREV PLPAGIYNLD DLKALGRRQG WCPYFLARYS ILHANVVVYS YHYLLDPKIA DLVSKELARK AVVVFDEAHN ID NVCIDSM SVNLTRRTLD RCQGNLETLQ KTVLRIKETD EQRLRDEYRR LVEG(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)VPGSIRT AEHFLGFLRR LLEYVKWRLR VQHVVQESPP AFLSGLAQRV CIQ RKPLRF CAERLRSLLH TLEITDLADF SPLTLLANFA TLVSTYAKGF TIIIEPFDDR TPTIANPILH FSCMDASLAI KPVF ERFQS VIITSGTLSP LDIYPKILDF HPVTMATFTM TLARVCLCPM IIGRGNDQVA ISSKFETRED IAVIRNYGNL LLEMS AVVP DGIVAFFTSY QYMESTVASW YEQGILENIQ RNKLLFIETQ DGAETSVALE KYQEACENGR GAILLSVARG KVSEGI DFV HHYGRAVIMF GVPYVYTQSR ILKARLEYLR DQFQIRENDF LTFDAMRHAA QCVGRAIRGK TDYGLMVFAD KRFARGD KR GKLPRWIQEH LTDANLNLTV DEGVQVAKYF LRQMAQPFHR EDQLGLSLLS LEQLESEETL KRIEQIAQQL

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Macromolecule #3: General transcription factor IIH subunit 1, p62

MacromoleculeName: General transcription factor IIH subunit 1, p62 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.789 KDa
SequenceString: MATSSEEVLL IVKKVRQKKQ DGALYLMAER IAWAPEGKDR FTISHMYADI KCQKISPEGK AKIQLQLVLH AGDTTNFHFS NESTAVKER DAVKDLLQQL LPKFKRKANK ELEEKNRMLQ EDPVLFQLYK DLVVSQVISA EEFWANRL(UNK)(UNK) (UNK)(UNK)(UNK) ...String:
MATSSEEVLL IVKKVRQKKQ DGALYLMAER IAWAPEGKDR FTISHMYADI KCQKISPEGK AKIQLQLVLH AGDTTNFHFS NESTAVKER DAVKDLLQQL LPKFKRKANK ELEEKNRMLQ EDPVLFQLYK DLVVSQVISA EEFWANRL(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)VRPQ TDGCN(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)SDIIESI FRTYPAVKMK YAENVPHNMT EKEFWTRFFQ SHYFHR(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)ENSNAA IIKRFNHHSA MVLAAGLRKQ EAQN EQTSE PSNMDGNSGD ADCFQPAVKR AKLQESIEYE DLG(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) IALNLKK SD RYYHGPTPI(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)TSQDI INSFQSIRQE MEAYTPKLTQ VLSSSAASST ITAL SPGGA LMQ(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)VPNDIQS ELKHLYVAVG ELLRH FWSC F(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)LVSHIE EMLQTAYNKL HTW(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)T

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Macromolecule #4: General transcription factor IIH subunit 4, p52

MacromoleculeName: General transcription factor IIH subunit 4, p52 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.245156 KDa
SequenceString: MESTPSRGLN RVHLQCRNLQ EFLGGLSPGV LDRLYGHPAT CLAVFRELPS LAKNWVMRML FLEQPLPQAA VALWVKKEFS KAQEESTGL LSGLRIWHTQ LLPGGLQGLI LNPIFRQNLR IALLGGGKAW SDDTSQLGPD KHARDVPSLD KYAEERWEVV L HFMVGSPS ...String:
MESTPSRGLN RVHLQCRNLQ EFLGGLSPGV LDRLYGHPAT CLAVFRELPS LAKNWVMRML FLEQPLPQAA VALWVKKEFS KAQEESTGL LSGLRIWHTQ LLPGGLQGLI LNPIFRQNLR IALLGGGKAW SDDTSQLGPD KHARDVPSLD KYAEERWEVV L HFMVGSPS AAVSQDLAQL LSQAGLMKST EPGEPPCITS AGFQFLLLDT PAQLWYFMLQ YLQTAQSRGM DLVEILSFLF QL SFSTLGK DYSVEGMSDS LLNFLQHLRE FGLVFQRKRK SRRYYPTRLA INLSSGVSGA GGTVHQPGFI VVETNYRLYA YTE SELQIA LIALFSEMLY RFPNMVVAQV TRESVQQAIA SGITAQQIIH FLRTRAHPVM LKQTPVLPPT ITDQIRLWEL ERDR LRFTE GVLYNQFLSQ VDFELLLAHA RELGVLVFEN SAKRLMVVTP AGHSDVKRFW KRQKHSS

UniProtKB: General transcription factor IIH subunit 4

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Macromolecule #5: General transcription factor IIH subunit 2, p44

MacromoleculeName: General transcription factor IIH subunit 2, p44 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.609098 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)GQV ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)GQV RLGMMRHLYV VVDGSRTMED QDLKPNRLTC TLKLLEYFVE EYFDQNPISQ IGIIVTKSKR AE KLTELSG NPRKHITSLK KAVDMTCHGE PSLYNSLSIA MQTLKHMPGH TSREVLIIFS SLTTCDPSNI YDLIKTLKAA KIR VSVIGL SAEVRVCTVL ARETGGTYHV ILDESHYKEL LTHHVSPPPA SSSSECSLIR MGFPQHTI(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)GGYFCPQCR AKYCELPVEC KICGLTLVSA PHLARSYHHL FPLDAFQEIP LEEYNGERFC YGCQGELKDQ H VYVCAVCQ NVFCVDCDVF VHDSLHCCPG CIH

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Macromolecule #6: General transcription factor IIH subunit 3, p34

MacromoleculeName: General transcription factor IIH subunit 3, p34 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.416008 KDa
SequenceString: MVSDEDELNL LVIVVDANPI WWGKQALKES QFTLSKCIDA VMVLGNSHLF MNRSNKLAVI ASHIQESRFL YPGKNGRLGD FFGDPGNPP EFNPSGSKDG KYELLTSANE VIVEEIKDLM TKSDIKGQHT ETLLAGSLAK ALCYIHRMNK EVKDNQEMKS R ILVIKAAE ...String:
MVSDEDELNL LVIVVDANPI WWGKQALKES QFTLSKCIDA VMVLGNSHLF MNRSNKLAVI ASHIQESRFL YPGKNGRLGD FFGDPGNPP EFNPSGSKDG KYELLTSANE VIVEEIKDLM TKSDIKGQHT ETLLAGSLAK ALCYIHRMNK EVKDNQEMKS R ILVIKAAE DSALQYMNFM NVIFAAQKQN ILIDACVLDS DSGLLQQACD ITGGLYLKVP QMPSLLQYLL WVFLPDQDQR SQ LILPPPV HVDYRAACFC HRNLIEIGYV CSVCLSIFCN FSPICTTCET AFKISLPPVL KAKKKKLKVS A

UniProtKB: General transcription factor IIH subunit 3

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Macromolecule #7: General transcription factor IIH subunit 5, p8

MacromoleculeName: General transcription factor IIH subunit 5, p8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.060362 KDa
SequenceString:
MVNVLKGVLI ECDPAMKQFL LYLDESNALG KKFIIQDIDD THVFVIAELV NVLQERVGEL MDQNAFSLTQ K

UniProtKB: General transcription factor IIH subunit 5

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Macromolecule #8: CDK-activating kinase assembly factor MAT1

MacromoleculeName: CDK-activating kinase assembly factor MAT1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.873965 KDa
SequenceString: MDDQGCPRCK TTKYRNPSLK LMVNVCGHTL CESCVDLLFV RGAGNCPECG TPLRKSNFRV QLFEDPTVDK EVEIRKKVLK IYNKREEDF PSLREYNDFL EEVEEIVFNL TNNVDLDNTK KKMEIYQKEN KDVIQKNKLK LTREQEELEE ALEVERQENE Q RRLFIQKE ...String:
MDDQGCPRCK TTKYRNPSLK LMVNVCGHTL CESCVDLLFV RGAGNCPECG TPLRKSNFRV QLFEDPTVDK EVEIRKKVLK IYNKREEDF PSLREYNDFL EEVEEIVFNL TNNVDLDNTK KKMEIYQKEN KDVIQKNKLK LTREQEELEE ALEVERQENE Q RRLFIQKE EQLQQILKRK NKQAFLDELE SSDLPVALLL AQHKDRSTQL EMQLEKPKPV KPVTFSTGIK MGQHISLAPI HK LEEALYE YQPLQIETYG PHVPELEMLG RLGYLNHVRA ASPQDLAGGY TSSLACHRAL QDAFSGLFWQ PS

UniProtKB: CDK-activating kinase assembly factor MAT1

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Macromolecule #9: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 9 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.0049 mg/mL
BufferpH: 7.9
Component:
ConcentrationName
20.0 mMHepes-KOH
150.0 mMSodium chloride
5.0 mMMagnesium chloride
0.015 %NP40 substitute
1.5 %Glycerol
2.0 %Trehalose
GridModel: C-flat / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Details: Gatan Solarus
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: A thin film of continuous carbon was floated onto Protochips C-flat CF-4/2 holey carbon grids and glow discharged or plasma cleaned before application of 4 uL of sample solution..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
DetailsResidual beam tilt corrected in RELION 3.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 7 / Number real images: 21437 / Average exposure time: 8.25 sec. / Average electron dose: 50.0 e/Å2
Details: Images were collected as dose-fractionated movie frames (33 or 50 frames per exposure).
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 43478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.7000000000000001 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3802

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 138659
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 8 / Avg.num./class: 100000 / Software - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial model
PDB IDChain

5of4

source_name: PDB, initial_model_type: experimental model

4ern

source_name: PDB, initial_model_type: experimental model

5oqj

source_name: PDB, initial_model_type: experimental model

1g25

source_name: PDB, initial_model_type: experimental model

5o85

source_name: PDB, initial_model_type: experimental model

2dii

source_name: PDB, initial_model_type: experimental model

2jnj

source_name: PDB, initial_model_type: experimental model
DetailsReference structures and homology models were docked and subsequently completely rebuilt according to the density. Parts of the structure were traced de novo.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6nmi:
Cryo-EM structure of the human TFIIH core complex

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