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- EMDB-22588: Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening -

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Basic information

Entry
Database: EMDB / ID: EMD-22588
TitleStructure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening
Map dataComposite map after multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA with separate refinement of TFIIH and Rad4-23-33/DNA bodies
Sample
  • Complex: 10 component complex of Rad4-23, Rad33 and TFIIH on damaged DNA
    • Protein or peptide: x 8 types
    • DNA: x 2 types
  • Protein or peptide: x 1 types
  • Ligand: x 3 types
Function / homology
Function and homology information


nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / SUMOylation of DNA damage response and repair proteins / positive regulation of mitotic recombination / DNA translocase activity ...nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / SUMOylation of DNA damage response and repair proteins / positive regulation of mitotic recombination / DNA translocase activity / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / transcription open complex formation at RNA polymerase II promoter / phosphatidylinositol-3-phosphate binding / 5'-3' DNA helicase activity / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / 3'-5' DNA helicase activity / transcription preinitiation complex / poly(A)+ mRNA export from nucleus / DNA duplex unwinding / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / 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 / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / ATPase activator activity / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / mismatch repair / transcription by RNA polymerase I / ATP-dependent activity, acting on DNA / DNA helicase activity / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / ubiquitin protein ligase activity / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rad33 / Rad33 / 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 ...Rad33 / Rad33 / 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 / Bacterial type XPD DNA helicase, FeS cluster domain / Transglutaminase-like superfamily / 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 / Helical and beta-bridge domain / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helical and beta-bridge domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / ATP-dependent helicase Rad3/Chl1-like / 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 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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 / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Papain-like cysteine peptidase 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 / PH-like domain superfamily / 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 / DNA repair protein RAD4 / General transcription and DNA repair factor IIH subunit TFB1 / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription and DNA repair factor IIH subunit TFB2 / DNA repair protein RAD33 / General transcription and DNA repair factor IIH subunit SSL1 / General transcription and DNA repair factor IIH subunit TFB4 / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.25 Å
Authorsvan Eeuwen T / Min JH / Murakami K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123233 United States
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair.
Authors: Trevor van Eeuwen / Yoonjung Shim / Hee Jong Kim / Tingting Zhao / Shrabani Basu / Benjamin A Garcia / Craig D Kaplan / Jung-Hyun Min / Kenji Murakami /
Abstract: The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor ...The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor complex, TFIIH, for subsequent lesion verification. Here, we present a cryo-EM structure of an NER initiation complex containing Rad4-Rad23-Rad33 (yeast homologue of XPC-RAD23B-CETN2) and 7-subunit coreTFIIH assembled on a carcinogen-DNA adduct lesion at 3.9-9.2 Å resolution. A ~30-bp DNA duplex could be mapped as it straddles between Rad4 and the Ssl2 (XPB) subunit of TFIIH on the 3' and 5' side of the lesion, respectively. The simultaneous binding with Rad4 and TFIIH was permitted by an unwinding of DNA at the lesion. Translocation coupled with torque generation by Ssl2 and Rad4 would extend the DNA unwinding at the lesion and deliver the damaged strand to Rad3 (XPD) in an open form suitable for subsequent lesion scanning and verification.
History
DepositionSep 3, 2020-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k04
  • Surface level: 0.0018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22588.png

Downloads & links

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Map

FileDownload / File: emd_22588.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map after multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA with separate refinement of TFIIH and Rad4-23-33/DNA bodies
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.00167 / Movie #1: 0.0018
Minimum - Maximum0.0 - 0.0066725616
Average (Standard dev.)8.202225e-05 (±0.00042812002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean0.0000.0070.000

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Supplemental data

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Additional map: Map of Rad4-23-33/DNA body from multibody refinement of...

Fileemd_22588_additional_1.map
AnnotationMap of Rad4-23-33/DNA body from multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map of TFIIH body from multibody refinement of...

Fileemd_22588_additional_2.map
AnnotationMap of TFIIH body from multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map of TFIIH body from multibody...

Fileemd_22588_half_map_1.map
AnnotationUnfiltered half map of TFIIH body from multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map of TFIIH body from multibody...

Fileemd_22588_half_map_2.map
AnnotationUnfiltered half map of TFIIH body from multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 10 component complex of Rad4-23, Rad33 and TFIIH on damaged DNA

EntireName: 10 component complex of Rad4-23, Rad33 and TFIIH on damaged DNA
Components
  • Complex: 10 component complex of Rad4-23, Rad33 and TFIIH on damaged DNA
    • Protein or peptide: DNA repair protein RAD33
    • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB2
    • Protein or peptide: DNA repair helicase RAD3
    • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB1
    • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB4
    • Protein or peptide: General transcription and DNA repair factor IIH subunit SSL1
    • DNA: Damaged DNA strand
    • DNA: Undamaged DNA strand
    • Protein or peptide: DNA repair protein RAD4
    • Protein or peptide: DNA repair helicase RAD25
  • Protein or peptide: RNA polymerase II transcription factor B subunit 5
  • Ligand: CALCIUM IONCalcium
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: ZINC ION

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Supramolecule #1: 10 component complex of Rad4-23, Rad33 and TFIIH on damaged DNA

SupramoleculeName: 10 component complex of Rad4-23, Rad33 and TFIIH on damaged DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10

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Macromolecule #1: DNA repair protein RAD33

MacromoleculeName: DNA repair protein RAD33 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 20.291457 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSKSTNVSYE RVELFENPKV PIEVEDEILE KYAESSLDHD MTVNELPRFF KDLQLEPTIW KLVRNEDVII EGTDVIDFTK LVRCTCQLL ILMNNLTVID DLWSMLIRNC GRDVDFPQVA LRDHVLSVKD LQKISNLIGA DQSSGTIEMI SCATDGKRLF M TYLDFGCV LGKLGYLKM

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Macromolecule #2: General transcription and DNA repair factor IIH subunit TFB2

MacromoleculeName: General transcription and DNA repair factor IIH subunit TFB2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 58.602312 KDa
SequenceString: MSDYSLKHSV TQYLEEIPQQ VQNRLYTSPA TCLAIYRILP PLAKFFIMAM VFNENEVPLL DLDKWVNSNG KLQFQNAIKS MKSLHLLIP NKSSGTLMIN LNPTFKISLR NALTGGEVQN SFGVVVEENV VSLDLLDEYS ANKWETILHF MVGTPLAKIP S EKVLNLLK ...String:
MSDYSLKHSV TQYLEEIPQQ VQNRLYTSPA TCLAIYRILP PLAKFFIMAM VFNENEVPLL DLDKWVNSNG KLQFQNAIKS MKSLHLLIP NKSSGTLMIN LNPTFKISLR NALTGGEVQN SFGVVVEENV VSLDLLDEYS ANKWETILHF MVGTPLAKIP S EKVLNLLK HSKLMEEVNS TGEFKITNEG FQFLLQEINS QLWTLLLQYL KMIETSKMDL VDVLHFIFML GALEVGKAYK ID ALSETQR IMLQDMRDYG LVFQKHSNDS IFYPTKLALM LTSDTKTIRS ASNAMDSVLR QNREEPSVNE DGANGKSTTD ITT SDDLNK AGLKNQDIPD GSLIVETNFK IYSYSNSPLQ IAVLSLFVHL KARFVNMVLG QITRESIRRA LTNGITADQI IAYL ETHAH PQMRRLAEEK LEKKLELDPN CKEPLQVLPP TVVDQIRLWQ LELDRVITYE GSLYSDFETS QEYNLLSKYA QDIGV LLWK DDKKKKFFIS KEGNSQVLDF AKRKLKKKQ

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Macromolecule #3: DNA repair helicase RAD3

MacromoleculeName: DNA repair helicase RAD3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 89.899047 KDa
SequenceString: MKFYIDDLPV LFPYPKIYPE QYNYMCDIKK TLDVGGNSIL EMPSGTGKTV SLLSLTIAYQ MHYPEHRKII YCSRTMSEIE KALVELENL MDYRTKELGY QEDFRGLGLT SRKNLCLHPE VSKERKGTVV DEKCRRMTNG QAKRKLEEDP EANVELCEYH E NLYNIEVE ...String:
MKFYIDDLPV LFPYPKIYPE QYNYMCDIKK TLDVGGNSIL EMPSGTGKTV SLLSLTIAYQ MHYPEHRKII YCSRTMSEIE KALVELENL MDYRTKELGY QEDFRGLGLT SRKNLCLHPE VSKERKGTVV DEKCRRMTNG QAKRKLEEDP EANVELCEYH E NLYNIEVE DYLPKGVFSF EKLLKYCEEK TLCPYFIVRR MISLCNIIIY SYHYLLDPKI AERVSNEVSK DSIVIFDEAH NI DNVCIES LSLDLTTDAL RRATRGANAL DERISEVRKV DSQKLQDEYE KLVQGLHSAD ILTDQEEPFV ETPVLPQDLL TEA IPGNIR RAEHFVSFLK RLIEYLKTRM KVLHVISETP KSFLQHLKQL TFIERKPLRF CSERLSLLVR TLEVTEVEDF TALK DIATF ATLISTYEEG FLLIIEPYEI ENAAVPNPIM RFTCLDASIA IKPVFERFSS VIITSGTISP LDMYPRMLNF KTVLQ KSYA MTLAKKSFLP MIITKGSDQV AISSRFEIRN DPSIVRNYGS MLVEFAKITP DGMVVFFPSY LYMESIVSMW QTMGIL DEV WKHKLILVET PDAQETSLAL ETYRKACSNG RGAILLSVAR GKVSEGIDFD HQYGRTVLMI GIPFQYTESR ILKARLE FM RENYRIREND FLSFDAMRHA AQCLGRVLRG KDDYGVMVLA DRRFSRKRSQ LPKWIAQGLS DADLNLSTDM AISNTKQF L RTMAQPTDPK DQEGVSVWSY EDLIKHQNSR KDQGGFIENE NKEGEQDEDE DEDIEMQ

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Macromolecule #4: General transcription and DNA repair factor IIH subunit TFB1

MacromoleculeName: General transcription and DNA repair factor IIH subunit TFB1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 72.959258 KDa
SequenceString: PSHSGAAIFE KVSGIIAINE DVSPAELTWR STDGDKVHTV VLSTIDKLQA TPASSEKMML RLIGKVDESK KRKDNEGNEV VPKPQRHMF SFNNRTVMDN IKMTLQQIIS RYKDADIYEE KRRREESAQH TETPMSSSSV TAGTPTPHLD TPQLNNGAPL I NTAKLDDS ...String:
PSHSGAAIFE KVSGIIAINE DVSPAELTWR STDGDKVHTV VLSTIDKLQA TPASSEKMML RLIGKVDESK KRKDNEGNEV VPKPQRHMF SFNNRTVMDN IKMTLQQIIS RYKDADIYEE KRRREESAQH TETPMSSSSV TAGTPTPHLD TPQLNNGAPL I NTAKLDDS LSKEKLLTNL KLQQSLLKGN KVLMKVFQET VINAGLPPSE FWSTRIPLLR AFALSTSQKV GPYNVLSTIK PV ASSENKV NVNLSREKIL NIFENYPIVK KAYTDNVPKN FKEPEFWARF FSSKLFRKLR GEKIMQNDRG DVIIDRYLTL DQE FDRKDD DMLLHPVKKI IDLDGNIQDD PVVRGNRPDF TMQPGVDING NSDGTVDILK GMNRLSEKMI MALKNEYSRT NLQN KSNIT NDEEDEDNDE RNELKIDDLN ESYKTNYAII HLKRNAHEKT TDNDAKSSAD SIKNADLKVS NQQMLQQLSL VMDNL INKL DLNQVVPNNE VSNKINKRVI TAIKINAKQA KHNNVNSALG SFVDNTSQAN ELEVKSTLPI DLLESCRMLH TTCCEF LKH FYIHFQSGEQ KQASTVKKLY NHLKDCIEKL NELFQDVLNG DGESMSNTCT AYLKPVLNSI TLATHKYDEY FNEYNNN SN

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Macromolecule #5: General transcription and DNA repair factor IIH subunit TFB4

MacromoleculeName: General transcription and DNA repair factor IIH subunit TFB4
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 37.506422 KDa
SequenceString: MDAISDPTFK HARSRKQVTE ESPSLLTVII EIAPKLWTTF DEEGNEKGSI IKVLEALIVF LNAHLAFNSA NKVAVIAAYS QGIKYLYPE STSALKASES ENKTRSDLKI INSDMYRRFR NVDETLVEEI YKLFELEKKQ IEQNSQRSTL AGAMSAGLTY V NRISKESV ...String:
MDAISDPTFK HARSRKQVTE ESPSLLTVII EIAPKLWTTF DEEGNEKGSI IKVLEALIVF LNAHLAFNSA NKVAVIAAYS QGIKYLYPE STSALKASES ENKTRSDLKI INSDMYRRFR NVDETLVEEI YKLFELEKKQ IEQNSQRSTL AGAMSAGLTY V NRISKESV TTSLKSRLLV LTCGSGSSKD EIFQYIPIMN CIFSATKMKC PIDVVKIGGS KESTFLQQTT DATNGVYLHV ES TEGLIQY LATAMFIDPS LRPIIVKPNH GSVDFRTSCY LTGRVVAVGF ICSVCLCVLS IIPPGNKCPA CDSQFDEHVI AKL KRKPVV PRLKAKKKVT KP

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Macromolecule #6: General transcription and DNA repair factor IIH subunit SSL1

MacromoleculeName: General transcription and DNA repair factor IIH subunit SSL1
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 52.370035 KDa
SequenceString: MAPVVISESE EDEDRVAITR RTKRQVHFDG EGDDRVDQQQ QQHSSSHRDR DKHVQRKKKK RLSNRNLQGS NGGYAWEDEI KRSWDLVKV DDEGDMASLV ASIVEARKKR TAKKNITPYQ RGIIRSLILT LDCSEAMLEK DLRPNRHAMI IQYAIDFVHE F FDQNPISQ ...String:
MAPVVISESE EDEDRVAITR RTKRQVHFDG EGDDRVDQQQ QQHSSSHRDR DKHVQRKKKK RLSNRNLQGS NGGYAWEDEI KRSWDLVKV DDEGDMASLV ASIVEARKKR TAKKNITPYQ RGIIRSLILT LDCSEAMLEK DLRPNRHAMI IQYAIDFVHE F FDQNPISQ MGIIIMRNGL AQLVSQVSGN PQDHIDALKS IRKQEPKGNP SLQNALEMAR GLLLPVPAHC TREVLIVFGS LS TTDPGDI HQTIDSLVSE KIRVKVLGLS AQVAICKELC KATNYGDESF YKILLDETHL KELFNEAVTP LPVNKINKGF TLV KMGFPT RIFEDTPTFC SCHSKLVYGG YFCPNCHSKV CSLPTVCPCC DLMLILSTHL ARSYHHLMPL KTFAEVPTTE KFRS EDCFS CQSRFPILKN HKNGKLLTSS RYRCEDCKQE FCVDCDVFIH EILHNCPGCE SKPVIT

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Macromolecule #9: DNA repair protein RAD4

MacromoleculeName: DNA repair protein RAD4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 87.374492 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNEDLPKEYF ELIRKALNEK EAEKAPLSRR RRVRRKNQPL PDAKKKFKTG LNELPRESVV TVNLDSSDDG VVTVPTDDSV EEIQSSEED YDSEEFEDVT DGNEVAGVED ISVEIKPSSK RNSDARRTSR NVCSNEERKR RKYFHMLYLV CLMVHGFIRN E WINSKRLS ...String:
MNEDLPKEYF ELIRKALNEK EAEKAPLSRR RRVRRKNQPL PDAKKKFKTG LNELPRESVV TVNLDSSDDG VVTVPTDDSV EEIQSSEED YDSEEFEDVT DGNEVAGVED ISVEIKPSSK RNSDARRTSR NVCSNEERKR RKYFHMLYLV CLMVHGFIRN E WINSKRLS RKLSNLVPEK VFELLHPQKD EELPLRSTRK LLDGLKKCME LWQKHWKITK KYDNEGLYMR TWKEIEMSAN NK RKFKTLK RSDFLRAVSK GHGDPDISVQ GFVAMLRACN VNARLIMSCQ PPDFTNMKID TSLNGNNAYK DMVKYPIFWC EVW DKFSKK WITVDPVNLK TIEQVRLHSK LAPKGVACCE RNMLRYVIAY DRKYGCRDVT RRYAQWMNSK VRKRRITKDD FGEK WFRKV ITALHHRKRT KIDDYEDQYF FRRDESEGIP DSVQDLKNHP YYVLEQDIKQ TQIVKPGCKE CGYLKVHGKV GKVLK VYAK RDIADLKSAR QWYMNGRILK TGSRCKKVIK RTVGRPKGEA EEEDERLYSF EDTELYIPPL ASASGEITKN TFGNIE VFA PTMIPGNCCL VENPVAIKAA RFLGVEFAPA VTSFKFERGS TVKPVLSGIV VAKWLREAIE TAIDGIEFIQ EDDNRKE HL LGALESWNTL LLKLRIRSKL NSTYGKIAEE EPNVTKEQNI ADNHDNTETF MGGGFLPGIA NHEARPYSEP SEPEDSLD Y VSVDKAEESA TDDDVGEDYS DFMKELEMSE ESD

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Macromolecule #10: DNA repair helicase RAD25

MacromoleculeName: DNA repair helicase RAD25 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 95.461664 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKD KALLQDTNSD IPADFVPDSV SGMFRSHDFS YLRLRPDHAS RPLWISPSDG RIILESFSPL AEQAQDFLVT I AEPISRPS ...String:
MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKD KALLQDTNSD IPADFVPDSV SGMFRSHDFS YLRLRPDHAS RPLWISPSDG RIILESFSPL AEQAQDFLVT I AEPISRPS HIHEYKITAY SLYAAVSVGL ETDDIISVLD RLSKVPVAES IINFIKGATI SYGKVKLVIK HNRYFVETTQ AD ILQMLLN DSVIGPLRID SDHQVQPPED VLQQQLQQTA GKPATNVNPN DVEAVFSAVI GGDNEREEED DDIDAVHSFE IAN ESVEVV KKRCQEIDYP VLEEYDFRND HRNPDLDIDL KPSTQIRPYQ EKSLSKMFGN GRARSGIIVL PCGAGKTLVG ITAA CTIKK SVIVLCTSSV SVMQWRQQFL QWCTLQPENC AVFTSDNKEM FQTESGLVVS TYSMVANTRN RSHDSQKVMD FLTGR EWGF IILDEVHVVP AAMFRRVVST IAAHAKLGLT ATLVREDDKI GDLNFLIGPK LYEANWMELS QKGHIANVQC AEVWCP MTA EFYQEYLRET ARKRMLLYIM NPTKFQACQF LIQYHERRGD KIIVFSDNVY ALQEYALKMG KPFIYGSTPQ QERMNIL QN FQYNDQINTI FLSKVGDTSI DLPEATCLIQ ISSHYGSRRQ EAQRLGRILR AKRRNDEGFN AFFYSLVSKD TQEMYYST K RQAFLVDQGY AFKVITHLHG MENIPNLAYA SPRERRELLQ EVLLKNEEAA GIEVGDDADN SVGRGSNGHK RFKSKAVRG EGSLSGLAGG EDMAYMEYST NKNKELKEHH PLIRKMYYKN LKK

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Macromolecule #11: RNA polymerase II transcription factor B subunit 5

MacromoleculeName: RNA polymerase II transcription factor B subunit 5 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 8.24349 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARARKGALV QCDPSIKALI LQIDAKMSDI VLEELDDTHL LVNPSKVEFV KHELNRLLSK NIYNPMDEEE NQ

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Macromolecule #7: Damaged DNA strand

MacromoleculeName: Damaged DNA strand / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.641573 KDa
SequenceString:
(DT)(DA)(DT)(DC)(DT)(DC)(DG)(DC)(DA)(DA) (DT)(DG)(T64)(DT)(DG)(DG)(DA)(DT)(DG) (DT)(DT)(DG)(DA)(DG)(DT)(DC)(DA)

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Macromolecule #8: Undamaged DNA strand

MacromoleculeName: Undamaged DNA strand / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.855751 KDa
SequenceString:
(DT)(DT)(DG)(DA)(DC)(DT)(DC)(DA)(DA)(DC) (DA)(DT)(DC)(DC)(DA)(DA)(DA)(DC)(DA)(DC) (DT)(DG)(DC)(DG)(DA)(DG)(DA)(DT)(DA)

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Macromolecule #12: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 12 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #13: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 13 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / Number of copies: 5 / 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

BufferpH: 7.6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC / Details: Manually blotted by Leica EM CPC.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 73146
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6cfi

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7k04:
Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening

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