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- EMDB-56566: Cryo-EM structure of the human holo-TFIIH-XPC complex bound to bu... -

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Basic information

Entry
Database: EMDB / ID: EMD-56566
TitleCryo-EM structure of the human holo-TFIIH-XPC complex bound to bulky lesion-mimic DNA (consensus map)
Map dataPost-processed, filtered cryo-EM map used for coordinate refinement
Sample
  • Complex: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.
    • Protein or peptide: x 11 types
    • DNA: x 2 types
  • Ligand: x 3 types
KeywordsNucleotide excision repair / DNA Repair / helicase / transcription factor / DNA BINDING PROTEIN
Function / homology
Function and homology information


heteroduplex DNA loop binding / nucleotide-excision repair factor 2 complex / XPC complex / nucleotide-excision repair complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA damage sensor activity / Cytosolic iron-sulfur cluster assembly ...heteroduplex DNA loop binding / nucleotide-excision repair factor 2 complex / XPC complex / nucleotide-excision repair complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA damage sensor activity / Cytosolic iron-sulfur cluster assembly / heterotrimeric G-protein binding / transcription export complex 2 / positive regulation of mitotic recombination / hair cell differentiation / response to auditory stimulus / nucleotide-excision repair factor 3 complex / histone H4K20 demethylase activity / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIK complex / nuclear pore nuclear basket / CAK-ERCC2 complex / bubble DNA binding / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / G protein-coupled receptor internalization / DNA 5'-3' helicase / nuclear thyroid hormone receptor binding / transcription preinitiation complex / sperm principal piece / RNA Polymerase I Transcription Termination / embryonic organ development / UV-damage excision repair / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / regulation of mitotic cell cycle phase transition / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / 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 / ATPase activator activity / centriole replication / proteasome binding / DNA topological change / RNA Polymerase I Transcription Initiation / response to UV / DNA 3'-5' helicase / 3'-5' DNA helicase activity / polyubiquitin modification-dependent protein binding / Tat-mediated elongation of the HIV-1 transcript / Cyclin E associated events during G1/S transition / Formation of HIV-1 elongation complex containing HIV-1 Tat / mismatch repair / SUMOylation of DNA damage response and repair proteins / Cyclin A:Cdk2-associated events at S phase entry / Formation of HIV elongation complex in the absence of HIV Tat / hormone-mediated signaling pathway / mRNA export from nucleus / Cyclin A/B1/B2 associated events during G2/M transition / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / regulation of G1/S transition of mitotic cell cycle / proteasome complex / transcription by RNA polymerase I / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / RNA Polymerase II Pre-transcription Events / Recruitment of mitotic centrosome proteins and complexes / centriole / Recruitment of NuMA to mitotic centrosomes / positive regulation of smooth muscle cell proliferation / Anchoring of the basal body to the plasma membrane / transcription-coupled nucleotide-excision repair / sperm midpiece / AURKA Activation by TPX2 / DNA helicase activity / regulation of cytokinesis / site of DNA damage / Josephin domain DUBs / TP53 Regulates Transcription of DNA Repair Genes / G1/S transition of mitotic cell cycle / ubiquitin binding / chromosome segregation / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / transcription elongation by RNA polymerase II / microtubule cytoskeleton organization
Similarity search - Function
Rad4 beta-hairpin domain 2 / RAD23A/RAD23B, UBA1 domain / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 ...Rad4 beta-hairpin domain 2 / RAD23A/RAD23B, UBA1 domain / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / : / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Transglutaminase-like superfamily / : / MAT1 C-terminal CAK anchor / 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 / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / 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 / Helical and beta-bridge domain / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Helical and beta-bridge domain / Transcription factor TFIIH complex subunit Tfb5 / ERCC3/RAD25/XPB helicase, C-terminal domain / : / ATP-dependent helicase Rad3/Chl1-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) / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / UBA/TS-N domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Ubiquitin associated domain / ATP-dependent RNA helicase DEAD-box, conserved site / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / 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. / Ring finger / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Papain-like cysteine peptidase superfamily / EF-hand domain pair / EF-hand, calcium binding motif / Zinc finger RING-type profile. / Zinc finger, RING-type / EF-Hand 1, calcium-binding site
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 / Centrin-2 / CDK-activating kinase assembly factor MAT1 / Lysine-specific demethylase RAD23B / DNA repair protein complementing XP-C cells / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.91 Å
Authorsde Martin Garrido N / Haste CAF / Feng J / Cronin NB / Greber BJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: Sci Adv / Year: 2026
Title: Visualization of stepwise derepression of TFIIH in global genome nucleotide excision repair.
Authors: Natàlia de Martín Garrido / Callum A F Haste / Junjie Feng / Nora B Cronin / Basil J Greber /
Abstract: Nucleotide excision repair (NER) is a crucial DNA repair pathway that is orchestrated by transcription factor IIH (TFIIH) in eukaryotic cells. TFIIH is a multifunctional complex that contains two DNA ...Nucleotide excision repair (NER) is a crucial DNA repair pathway that is orchestrated by transcription factor IIH (TFIIH) in eukaryotic cells. TFIIH is a multifunctional complex that contains two DNA helicase/DNA translocase subunits and a kinase module, different subsets of which act in NER, transcription initiation, and cell cycle control. To ensure fidelity despite multifunctionality, the DNA helicase activity of TFIIH is autoinhibited in its free form or when the factor engages in transcription initiation. While the release of the kinase module has been identified as a key step in TFIIH activation, the molecular mechanisms controlling this step and concomitant structural changes in TFIIH are incompletely understood. Here, we determine high-resolution structures of three NER intermediates that visualize how TFIIH arrives at sites of DNA damage in an autoinhibited state and how autoinhibition is released via previously undescribed intermediates. These findings contribute to a mechanistic understanding of human DNA repair.
History
DepositionFeb 4, 2026-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56566.png

Downloads & links

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Map

FileDownload / File: emd_56566.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed, filtered cryo-EM map used for coordinate refinement
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 280 pix.
= 375.2 Å		1.34 Å/pix.
x 280 pix.
= 375.2 Å		1.34 Å/pix.
x 280 pix.
= 375.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00953
Minimum - Maximum-0.039846785 - 0.06741594
Average (Standard dev.)0.000027971442 (±0.0017385343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 375.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56566_msk_1.map
Projections & Slices
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Half map: Unfiltered, unsharpened cryo-EM half-map

Fileemd_56566_half_map_1.map
AnnotationUnfiltered, unsharpened cryo-EM half-map
Projections & Slices
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Half map: Unfiltered, unsharpened cryo-EM half-map

Fileemd_56566_half_map_2.map
AnnotationUnfiltered, unsharpened cryo-EM half-map
Projections & Slices
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Sample components

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Entire : Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.

EntireName: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.
Components
  • Complex: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPB
    • 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: General transcription factor IIH subunit 2
    • Protein or peptide: General transcription factor IIH subunit 3
    • Protein or peptide: General transcription factor IIH subunit 5
    • Protein or peptide: CDK-activating kinase assembly factor MAT1
    • Protein or peptide: DNA repair protein complementing XP-C cells
    • Protein or peptide: Lysine-specific demethylase RAD23B
    • Protein or peptide: Centrin-2
    • DNA: DNA (Cy5)
    • DNA: DNA (biotinylated)
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.

SupramoleculeName: Human holo-TFIIH, XPC complex, and XPA with biotinylated DNA.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 / Details: XPA is not observed in this reconstruction.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 726.82 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: 91.300711 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHENLY FQSNAMGKRD RADRDKKKSR KRHYEDEEDD EEDAPGNDPQ EAVPSAAGKQ VDESGTKVDE YGAKDYRLQM PLKDDHTSR PLWVAPDGHI FLEAFSPVYK YAQDFLVAIA EPVCRPTHVH EYKLTAYSLY AAVSVGLQTS DITEYLRKLS K TGVPDGIM ...String:
HHHHHHENLY FQSNAMGKRD RADRDKKKSR KRHYEDEEDD EEDAPGNDPQ EAVPSAAGKQ VDESGTKVDE YGAKDYRLQM PLKDDHTSR PLWVAPDGHI FLEAFSPVYK YAQDFLVAIA EPVCRPTHVH EYKLTAYSLY AAVSVGLQTS DITEYLRKLS K TGVPDGIM QFIKLCTVSY GKVKLVLKHN RYFVESCHPD VIQHLLQDPV IRECRLRNSE GEATELITET FTSKSAISKT AE SSGGPST SRVTDPQGKS DIPMDLFDFY EQMDKDEEEE EETQTVSFEV KQEMIEELQK RCIHLEYPLL AEYDFRNDSV NPD INIDLK PTAVLRPYQE KSLRKMFGNG RARSGVIVLP CGAGKSLVGV TAACTVRKRC LVLGNSAVSV EQWKAQFKMW STID DSQIC RFTSDAKDKP IGCSVAISTY SMLGHTTKRS WEAERVMEWL KTQEWGLMIL DEVHTIPAKM FRRVLTIVQA HCKLG LTAT LVREDDKIVD LNFLIGPKLY EANWMELQNN GYIAKVQCAE VWCPMSPEFY REYVAIKTKK RILLYTMNPN KFRACQ FLI KFHERRNDKI IVFADNVFAL KEYAIRLNKP YIYGPTSQGE RMQILQNFKH NPKINTIFIS KVGDTSFDLP EANVLIQ IS SHGGSRRQEA QRLGRVLRAK KGMVAEEYNA FFYSLVSQDT QEMAYSTKRQ RFLVDQGYSF KVITKLAGME EEDLAFST K EEQQQLLQKV LAATDLDAEE EVVAGEFGSR SSQASRRFGT MSSMSGADDT VYMEYHSSRS KAPSKHVHPL FKRFRK

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

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Macromolecule #2: TFIIH basal transcription factor complex helicase XPD subunit

MacromoleculeName: TFIIH basal transcription factor complex helicase XPD subunit
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.306305 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 RIEQIAQQLS SNDYKDDDDK

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

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Macromolecule #3: General transcription factor IIH subunit 1

MacromoleculeName: General transcription factor IIH subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.403961 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 MKKTGSGGEN LYFQSG SWS HPQFEKGGGS GGGSGGGSWS HPQFEKSG

UniProtKB: General transcription factor IIH subunit 1

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Macromolecule #4: General transcription factor IIH subunit 4

MacromoleculeName: General transcription factor IIH subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.245156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

MacromoleculeName: General transcription factor IIH subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.481996 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #6: General transcription factor IIH subunit 3

MacromoleculeName: General transcription factor IIH subunit 3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.416008 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

MacromoleculeName: General transcription factor IIH subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.060362 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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: DNA repair protein complementing XP-C cells

MacromoleculeName: DNA repair protein complementing XP-C cells / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 106.142203 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MARKRAAGGE PRGRELRSQK SKAKSKARRE EEEEDAFEDE KPPKKSLLSK VSQGKRKRGC SHPGGSADGP AKKKVAKVTV KSENLKVIK DEALSDGDDL RDFPSDLKKA HHLKRGATMN EDSNEEEEES ENDWEEVEEL SEPVLGDVRE STAFSRSLLP V KPVEIEIE ...String:
MARKRAAGGE PRGRELRSQK SKAKSKARRE EEEEDAFEDE KPPKKSLLSK VSQGKRKRGC SHPGGSADGP AKKKVAKVTV KSENLKVIK DEALSDGDDL RDFPSDLKKA HHLKRGATMN EDSNEEEEES ENDWEEVEEL SEPVLGDVRE STAFSRSLLP V KPVEIEIE TPEQAKTRER SEKIKLEFET YLRRAMKRFN KGVHEDTHKV HLLCLLANGF YRNNICSQPD LHAIGLSIIP AR FTRVLPR DVDTYYLSNL VKWFIGTFTV NAELSASEQD NLQTTLERRF AIYSARDDEE LVHIFLLILR ALQLLTRLVL SLQ PIPLKS ATAKGKKPSK ERLTADPGGS SETSSQVLEN HTKPKTSKGT KQEETFAKGT CRPSAKGKRN KGGRKKRSKP SSSE EDEGP GDKQEKATQR RPHGRERRVA SRVSYKEESG SDEAGSGSDF ELSSGEASDP SDEDSEPGPP KQRKAPAPQR TKAGS KSAS RTHRGSHRKD PSLPAASSSS SSSKRGKKMC SDGEKAEKRS IAGIDQWLEV FCEQEEKWVC VDCVHGVVGQ PLTCYK YAT KPMTYVVGID SDGWVRDVTQ RYDPVWMTVT RKCRVDAEWW AETLRPYQSP FMDREKKEDL EFQAKHMDQP LPTAIGL YK NHPLYALKRH LLKYEAIYPE TAAILGYCRG EAVYSRDCVH TLHSRDTWLK KARVVRLGEV PYKMVKGFSN RARKARLA E PQLREENDLG LFGYWQTEEY QPPVAVDGKV PRNEFGNVYL FLPSMMPIGC VQLNLPNLHR VARKLDIDCV QAITGFDFH GGYSHPVTDG YIVCEEFKDV LLTAWENEQA VIERKEKEKK EKRALGNWKL LAKGLLIRER LKRRYGPKSE AAAPHTDAGG GLSSDEEEG TSSQAEAARI LAASWPQNRE DEEKQKLKGG PKKTKREKKA AASHLFPFEQ L

UniProtKB: DNA repair protein complementing XP-C cells

+
Macromolecule #10: Lysine-specific demethylase RAD23B

MacromoleculeName: Lysine-specific demethylase RAD23B / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.203914 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQVTLKTLQQ QTFKIDIDPE ETVKALKEKI ESEKGKDAFP VAGQKLIYAG KILNDDTALK EYKIDEKNFV VVMVTKPKAV STPAPATTQ QSAPASTTAV TSSTTTTVAQ APTPVPALAP TSTPASITPA SATASSEPAP ASAAKQEKPA EKPAETPVAT S PTATDSTS ...String:
MQVTLKTLQQ QTFKIDIDPE ETVKALKEKI ESEKGKDAFP VAGQKLIYAG KILNDDTALK EYKIDEKNFV VVMVTKPKAV STPAPATTQ QSAPASTTAV TSSTTTTVAQ APTPVPALAP TSTPASITPA SATASSEPAP ASAAKQEKPA EKPAETPVAT S PTATDSTS GDSSRSNLFE DATSALVTGQ SYENMVTEIM SMGYEREQVI AALRASFNNP DRAVEYLLMG IPGDRESQAV VD PPQAAST GAPQSSAVAA AAATTTATTT TTSSGGHPLE FLRNQPQFQQ MRQIIQQNPS LLPALLQQIG RENPQLLQQI SQH QEHFIQ MLNEPVQEAG GQGGGGGGGS GGIAEAGSGH MNYIQVTPQE KEAIERLKAL GFPEGLVIQA YFACEKNENL AANF LLQQN FDED

UniProtKB: Lysine-specific demethylase RAD23B

+
Macromolecule #11: Centrin-2

MacromoleculeName: Centrin-2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.769486 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNFKKANM ASSSQRKRMS PKPELTEEQK QEIREAFDLF DADGTGTIDV KELKVAMRAL GFEPKKEEIK KMISEIDKEG TGKMNFGDF LTVMTQKMSE KDTKEEILKA FKLFDDDETG KISFKNLKRV AKELGENLTD EELQEMIDEA DRDGDGEVSE Q EFLRIMKK TSLY

UniProtKB: Centrin-2

+
Macromolecule #12: DNA (Cy5)

MacromoleculeName: DNA (Cy5) / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 21.483094 KDa
SequenceString: (DC)(DC)(DA)(DT)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DC)(DT)(DA)(DT)(DA)(DC)(DC)(DC) (DA)(DT)(DT)(DC)(DC)(DA)(DA)(DC)(DC) (DA)(DT)(DC)(DC)(DC)(DA)(DC)(DT)(DA)(DC) (DC) (VM6)(DT)(DC)(DC)(DA)(DT) ...String:
(DC)(DC)(DA)(DT)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DC)(DT)(DA)(DT)(DA)(DC)(DC)(DC) (DA)(DT)(DT)(DC)(DC)(DA)(DA)(DC)(DC) (DA)(DT)(DC)(DC)(DC)(DA)(DC)(DT)(DA)(DC) (DC) (VM6)(DT)(DC)(DC)(DA)(DT)(DC)(DT) (DT)(DC)(DA)(DC)(DT)(DC)(DA)(DA)(DC)(DT) (DA) (DT)(DC)(DA)(DC)(DC)(DC)(DT)(DA) (DA)(DT)(DA)(DC)

+
Macromolecule #13: DNA (biotinylated)

MacromoleculeName: DNA (biotinylated) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 29.197684 KDa
SequenceString: (DA)(DG)(DA)(DG)(DA)(DA)(DG)(DG)(DA)(DG) (DA)(DG)(DG)(DC)(DA)(DA)(DG)(DG)(DA)(DA) (DG)(DT)(DA)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DG)(DA)(DT)(DA)(DG)(DT)(DT)(DG)(DA) (DG) (DT)(DG)(DA)(DA)(DG)(DA) ...String:
(DA)(DG)(DA)(DG)(DA)(DA)(DG)(DG)(DA)(DG) (DA)(DG)(DG)(DC)(DA)(DA)(DG)(DG)(DA)(DA) (DG)(DT)(DA)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DG)(DA)(DT)(DA)(DG)(DT)(DT)(DG)(DA) (DG) (DT)(DG)(DA)(DA)(DG)(DA)(DT)(DG) (DG)(DA)(DC)(DA)(DG)(DG)(DT)(DA)(DG)(DT) (DG)(DG) (DG)(DA)(DT)(DG)(DG)(DT)(DT) (DG)(DG)(DA)(DA)(DT)(DG)(DG)(DG)(DT)(DA) (DT)(DA)(DG) (DG)(DT)(DA)(DT)(DA)(DG) (DG)(DG)(DA)(DT)(DG)(DG)

+
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

+
Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #16: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 16 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 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

Concentration0.16 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPES-KOHHepes
150.0 mMKClPotassium chloride
0.5 mMTCEPTris(2-carboxyethyl)phosphine hydrochloride
2.0 mMMgCl2Magnesium chloride
3.0 % (w/v)TrehaloseTrehalose
0.01 % (v/v)NP-40NP-40
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Details: Streptavidin affinity support grid
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP / Details: Leica EM GP2.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
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

Particle selectionNumber selected: 2426407
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

27996

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.0) / Number images used: 166008
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 5.0.0)

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