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- EMDB-12616: TFIIH in a post-translocated state (with ADP-BeF3) -

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Basic information

Entry
Database: EMDB / ID: EMD-12616
TitleTFIIH in a post-translocated state (with ADP-BeF3)
Map dataLocal resolution filtered and sharpened map
Sample
  • Complex: TFIIH (with ADP-BeF3)
    • Protein or peptide: x 11 types
    • DNA: x 2 types
  • Ligand: x 5 types
KeywordsInitiation / TRANSCRIPTION
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 / transcription factor TFIIE complex / 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 / transcription factor TFIIE complex / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / ventricular system development / CAK-ERCC2 complex / transcription factor TFIIK complex / UV protection / embryonic cleavage / DNA 5'-3' helicase / adult heart development / regulation of cyclin-dependent protein serine/threonine kinase activity / G protein-coupled receptor internalization / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / DNA 3'-5' helicase / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / erythrocyte maturation / 3'-5' DNA helicase activity / hematopoietic stem cell proliferation / spinal cord development / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / bone mineralization / mRNA Capping / ATPase activator activity / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / RNA Polymerase I Transcription Initiation / regulation of G1/S transition of mitotic cell cycle / RNA polymerase II transcribes snRNA genes / hematopoietic stem cell differentiation / embryonic organ development / Tat-mediated elongation of the HIV-1 transcript / 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 / Cyclin E associated events during G1/S transition / response to UV / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / transcription by RNA polymerase I / cyclin-dependent protein kinase holoenzyme complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / hormone-mediated signaling pathway / transcription-coupled nucleotide-excision repair / RNA Polymerase II Pre-transcription Events / extracellular matrix organization / positive regulation of smooth muscle cell proliferation / DNA helicase activity / 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 / nucleotide-excision repair / chromosome segregation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / cellular response to gamma radiation / G1/S transition of mitotic cell cycle / response to calcium ion / NoRC negatively regulates rRNA expression / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / spindle / multicellular organism growth / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / intracellular protein localization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 4 iron, 4 sulfur cluster binding / response to oxidative stress
Similarity search - Function
Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / 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 ...Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / 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 / ATP-dependent helicase Rad3/Chl1-like / : / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / 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) / 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. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Zinc finger, TFIIB-type / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / TFIIB zinc-binding / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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 / PH-like domain superfamily / helicase superfamily c-terminal domain / 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 IIE subunit 1 / 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) / Human mastadenovirus C
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsAibara S / Schilbach S
Funding support Germany, 5 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission894862 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
European Research Council (ERC)882357 Germany
CitationJournal: Nature / Year: 2021
Title: Structures of mammalian RNA polymerase II pre-initiation complexes.
Authors: Shintaro Aibara / Sandra Schilbach / Patrick Cramer /
Abstract: The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation.
History
DepositionMar 16, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 13.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nvx
  • Surface level: 13.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12616.png

Downloads & links

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Map

FileDownload / File: emd_12616.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered and sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 450 pix.
= 472.5 Å		1.05 Å/pix.
x 450 pix.
= 472.5 Å		1.05 Å/pix.
x 450 pix.
= 472.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 13.5 / Movie #1: 13.5
Minimum - Maximum-75.189229999999995 - 116.291079999999994
Average (Standard dev.)-0.0021994866 (±0.9634325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 472.49997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z472.500472.500472.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-75.189116.291-0.002

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Supplemental data

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Mask #1

Fileemd_12616_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: local resolution filtered map, unsharpened

Fileemd_12616_additional_1.map
Annotationlocal resolution filtered map, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 1

Fileemd_12616_half_map_1.map
AnnotationUnfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 2

Fileemd_12616_half_map_2.map
AnnotationUnfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : TFIIH (with ADP-BeF3)

EntireName: TFIIH (with ADP-BeF3)
Components
  • Complex: TFIIH (with ADP-BeF3)
    • Protein or peptide: TFIIH basal transcription factor complex helicase XPD subunit
    • Protein or peptide: General transcription factor IIH subunit 1
    • Protein or peptide: General transcription factor IIH subunit 4
    • Protein or peptide: CDK-activating kinase assembly factor MAT1
    • Protein or peptide: General transcription factor IIH subunit 3
    • Protein or peptide: General transcription factor IIH subunit 5
    • Protein or peptide: General transcription factor IIH subunit 2
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPB
    • DNA: Non-template DNA
    • DNA: Template DNA
    • Protein or peptide: General transcription factor IIE subunit 1
    • Protein or peptide: Unassigned Peptide, likely XPB
    • Protein or peptide: Unassigned Peptide, likely TFIIE-Beta
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: TFIIH (with ADP-BeF3)

SupramoleculeName: TFIIH (with ADP-BeF3) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Molecular weightTheoretical: 490 KDa

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Macromolecule #1: TFIIH basal transcription factor complex helicase XPD subunit

MacromoleculeName: TFIIH basal transcription factor complex helicase XPD subunit
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.021078 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 LVEGLREASA ARETDAHLAN PVLPDEVLQE AVP GSIRTA EHFLGFLRRL LEYVKWRLRV QHVVQESPPA FLSGLAQRVC IQRKPLRFCA ERLRSLLHTL EITDLADFSP LTLL ANFAT LVSTYAKGFT IIIEPFDDRT PTIANPILHF SCMDASLAIK PVFERFQSVI ITSGTLSPLD IYPKILDFHP VTMAT FTMT LARVCLCPMI IGRGNDQVAI SSKFETREDI AVIRNYGNLL LEMSAVVPDG IVAFFTSYQY MESTVASWYE QGILEN IQR NKLLFIETQD GAETSVALEK YQEACENGRG AILLSVARGK VSEGIDFVHH YGRAVIMFGV PYVYTQSRIL KARLEYL RD QFQIRENDFL TFDAMRHAAQ CVGRAIRGKT DYGLMVFADK RFARGDKRGK LPRWIQEHLT DANLNLTVDE GVQVAKYF L RQMAQPFHRE DQLGLSLLSL EQLESEETLK RIEQIAQQL

UniProtKB: General transcription and DNA repair factor IIH helicase subunit XPD

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Macromolecule #2: General transcription factor IIH subunit 1

MacromoleculeName: General transcription factor IIH subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.116492 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MATSSEEVLL IVKKVRQKKQ DGALYLMAER IAWAPEGKDR FTISHMYADI KCQKISPEGK AKIQLQLVLH AGDTTNFHFS NESTAVKER DAVKDLLQQL LPKFKRKANK ELEEKNRMLQ EDPVLFQLYK DLVVSQVISA EEFWANRLNV NATDSSSTSN H KQDVGISA ...String:
MATSSEEVLL IVKKVRQKKQ DGALYLMAER IAWAPEGKDR FTISHMYADI KCQKISPEGK AKIQLQLVLH AGDTTNFHFS NESTAVKER DAVKDLLQQL LPKFKRKANK ELEEKNRMLQ EDPVLFQLYK DLVVSQVISA EEFWANRLNV NATDSSSTSN H KQDVGISA AFLADVRPQT DGCNGLRYNL TSDIIESIFR TYPAVKMKYA ENVPHNMTEK EFWTRFFQSH YFHRDRLNTG SK DLFAECA KIDEKGLKTM VSLGVKNPLL DLTALEDKPL DEGYGISSVP SASNSKSIKE NSNAAIIKRF NHHSAMVLAA GLR KQEAQN EQTSEPSNMD GNSGDADCFQ PAVKRAKLQE SIEYEDLGKN NSVKTIALNL KKSDRYYHGP TPIQSLQYAT SQDI INSFQ SIRQEMEAYT PKLTQVLSSS AASSTITALS PGGALMQGGT QQAINQMVPN DIQSELKHLY VAVGELLRHF WSCFP VNTP FLEEKVVKMK SNLERFQVTK LCPFQEKIRR QYLSTNLVSH IEEMLQTAYN KLHTWQSRRL MKKT

UniProtKB: General transcription factor IIH subunit 1

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Macromolecule #3: General transcription factor IIH subunit 4

MacromoleculeName: General transcription factor IIH subunit 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.245156 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #4: CDK-activating kinase assembly factor MAT1

MacromoleculeName: CDK-activating kinase assembly factor MAT1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.873965 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #5: General transcription factor IIH subunit 3

MacromoleculeName: General transcription factor IIH subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.416008 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #6: General transcription factor IIH subunit 5

MacromoleculeName: General transcription factor IIH subunit 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.060362 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MVNVLKGVLI ECDPAMKQFL LYLDESNALG KKFIIQDIDD THVFVIAELV NVLQERVGEL MDQNAFSLTQ K

UniProtKB: General transcription factor IIH subunit 5

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Macromolecule #7: General transcription factor IIH subunit 2

MacromoleculeName: General transcription factor IIH subunit 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.481996 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDEEPERTKR WEGGYERTWE ILKEDESGSL KATIEDILFK AKRKRVFEHH GQVRLGMMRH LYVVVDGSRT MEDQDLKPNR LTCTLKLLE YFVEEYFDQN PISQIGIIVT KSKRAEKLTE LSGNPRKHIT SLKKAVDMTC HGEPSLYNSL SIAMQTLKHM P GHTSREVL ...String:
MDEEPERTKR WEGGYERTWE ILKEDESGSL KATIEDILFK AKRKRVFEHH GQVRLGMMRH LYVVVDGSRT MEDQDLKPNR LTCTLKLLE YFVEEYFDQN PISQIGIIVT KSKRAEKLTE LSGNPRKHIT SLKKAVDMTC HGEPSLYNSL SIAMQTLKHM P GHTSREVL IIFSSLTTCD PSNIYDLIKT LKAAKIRVSV IGLSAEVRVC TVLARETGGT YHVILDESHY KELLTHHVSP PP ASSSSEC SLIRMGFPQH TIASLSDQDA KPSFSMAHLD GNTEPGLTLG GYFCPQCRAK YCELPVECKI CGLTLVSAPH LAR SYHHLF PLDAFQEIPL EEYNGERFCY GCQGELKDQH VYVCAVCQNV FCVDCDVFVH DSLHCCPGCI HKIPAPSGV

UniProtKB: General transcription factor IIH subunit 2

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Macromolecule #8: 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: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.404734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGKRDRADRD KKKSRKRHYE DEEDDEEDAP GNDPQEAVPS AAGKQVDESG TKVDEYGAKD YRLQMPLKDD HTSRPLWVAP DGHIFLEAF SPVYKYAQDF LVAIAEPVCR PTHVHEYKLT AYSLYAAVSV GLQTSDITEY LRKLSKTGVP DGIMQFIKLC T VSYGKVKL ...String:
MGKRDRADRD KKKSRKRHYE DEEDDEEDAP GNDPQEAVPS AAGKQVDESG TKVDEYGAKD YRLQMPLKDD HTSRPLWVAP DGHIFLEAF SPVYKYAQDF LVAIAEPVCR PTHVHEYKLT AYSLYAAVSV GLQTSDITEY LRKLSKTGVP DGIMQFIKLC T VSYGKVKL VLKHNRYFVE SCHPDVIQHL LQDPVIRECR LRNSEGEATE LITETFTSKS AISKTAESSG GPSTSRVTDP QG KSDIPMD LFDFYEQMDK DEEEEEETQT VSFEVKQEMI EELQKRCIHL EYPLLAEYDF RNDSVNPDIN IDLKPTAVLR PYQ EKSLRK MFGNGRARSG VIVLPCGAGK SLVGVTAACT VRKRCLVLGN SAVSVEQWKA QFKMWSTIDD SQICRFTSDA KDKP IGCSV AISTYSMLGH TTKRSWEAER VMEWLKTQEW GLMILDEVHT IPAKMFRRVL TIVQAHCKLG LTATLVREDD KIVDL NFLI GPKLYEANWM ELQNNGYIAK VQCAEVWCPM SPEFYREYVA IKTKKRILLY TMNPNKFRAC QFLIKFHERR NDKIIV FAD NVFALKEYAI RLNKPYIYGP TSQGERMQIL QNFKHNPKIN TIFISKVGDT SFDLPEANVL IQISSHGGSR RQEAQRL GR VLRAKKGMVA EEYNAFFYSL VSQDTQEMAY STKRQRFLVD QGYSFKVITK LAGMEEEDLA FSTKEEQQQL LQKVLAAT D LDAEEEVVAG EFGSRSSQAS RRFGTMSSMS GADDTVYMEY HSSRSKAPSK HVHPLFKRFR K

UniProtKB: General transcription and DNA repair factor IIH helicase/translocase subunit XPB

+
Macromolecule #11: General transcription factor IIE subunit 1

MacromoleculeName: General transcription factor IIE subunit 1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.544102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADPDVLTEV PAALKRLAKY VIRGFYGIEH ALALDILIRN SCVKEEDMLE LLKFDRKQLR SVLNNLKGDK FIKCRMRVET AADGKTTRH NYYFINYRTL VNVVKYKLDH MRRRIETDER DSTNRASFKC PVCSSTFTDL EANQLFDPMT GTFRCTFCHT E VEEDESAM ...String:
MADPDVLTEV PAALKRLAKY VIRGFYGIEH ALALDILIRN SCVKEEDMLE LLKFDRKQLR SVLNNLKGDK FIKCRMRVET AADGKTTRH NYYFINYRTL VNVVKYKLDH MRRRIETDER DSTNRASFKC PVCSSTFTDL EANQLFDPMT GTFRCTFCHT E VEEDESAM PKKDARTLLA RFNEQIEPIY ALLRETEDVN LAYEILEPEP TEIPALKQSK DHAATTAGAA SLAGGHHREA WA TKGPSYE DLYTQNVVIN MDDQEDLHRA SLEGKSAKER PIWLRESTVQ GAYGSEDMKE GGIDMDAFQE REEGHAGPDD NEE VMRALL IHEKKTSSAM AGSVGAAAPV TAANGDDSES ETSESDDDSP PRPAAVAVHK REEDEEEDDE FEEVADDPIV MVAG RPFSY SEVSQRPELV AQMTPEEKEA YIAMGQRMFE DLFE

UniProtKB: General transcription factor IIE subunit 1

+
Macromolecule #12: Unassigned Peptide, likely XPB

MacromoleculeName: Unassigned Peptide, likely XPB / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 698.854 Da
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #13: Unassigned Peptide, likely TFIIE-Beta

MacromoleculeName: Unassigned Peptide, likely TFIIE-Beta / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.379692 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #9: Non-template DNA

MacromoleculeName: Non-template DNA / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human mastadenovirus C
Molecular weightTheoretical: 32.911859 KDa
SequenceString: (DC)(DG)(DG)(DG)(DT)(DG)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DA)(DG)(DG)(DG)(DG)(DG)(DG) (DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG) (DG)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG) (DC) (DG)(DC)(DG)(DT)(DT)(DC) ...String:
(DC)(DG)(DG)(DG)(DT)(DG)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DA)(DG)(DG)(DG)(DG)(DG)(DG) (DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG) (DG)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG) (DC) (DG)(DC)(DG)(DT)(DT)(DC)(DG)(DT) (DC)(DC)(DT)(DC)(DA)(DC)(DT)(DC)(DT)(DC) (DT)(DT) (DC)(DC)(DG)(DC)(DA)(DT)(DC) (DG)(DC)(DT)(DG)(DT)(DC)(DT)(DG)(DC)(DG) (DA)(DG)(DG) (DG)(DC)(DC)(DA)(DG)(DC) (DT)(DG)(DT)(DT)(DG)(DG)(DG)(DG)(DT)(DG) (DA)(DG)(DT)(DA) (DC)(DT)(DC)(DC)(DC) (DT)

GENBANK: GENBANK: MK041240.1

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Macromolecule #10: Template DNA

MacromoleculeName: Template DNA / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human mastadenovirus C
Molecular weightTheoretical: 32.508752 KDa
SequenceString: (DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DC)(DT) (DC)(DA)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DC)(DC)(DC)(DT) (DC)(DG)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DC) (DG) (DA)(DT)(DG)(DC)(DG)(DG) ...String:
(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DC)(DT) (DC)(DA)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DC)(DC)(DC)(DT) (DC)(DG)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DC) (DG) (DA)(DT)(DG)(DC)(DG)(DG)(DA)(DA) (DG)(DA)(DG)(DA)(DG)(DT)(DG)(DA)(DG)(DG) (DA)(DC) (DG)(DA)(DA)(DC)(DG)(DC)(DG) (DC)(DC)(DC)(DC)(DC)(DA)(DC)(DC)(DC)(DC) (DC)(DT)(DT) (DT)(DT)(DA)(DT)(DA)(DG) (DC)(DC)(DC)(DC)(DC)(DC)(DT)(DT)(DC)(DA) (DG)(DG)(DA)(DA) (DC)(DA)(DC)(DC)(DC) (DG)

GENBANK: GENBANK: MK041240.1

+
Macromolecule #14: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 14 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #16: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 16 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #17: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #18: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 399246
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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