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- EMDB-27997: XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5) -

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Basic information

Entry
Database: EMDB / ID: EMD-27997
TitleXPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5)
Map data
Sample
  • Complex: protein DNA complex
    • Protein or peptide: x 10 types
    • DNA: x 2 types
  • Ligand: x 3 types
Keywordsprotein-DNA complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / 9+2 motile cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / Cytosolic iron-sulfur cluster assembly / heterotrimeric G-protein binding ...nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / 9+2 motile cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / Cytosolic iron-sulfur cluster assembly / heterotrimeric G-protein binding / central nervous system myelin formation / transcription export complex 2 / response to auditory stimulus / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / nucleotide-excision repair, preincision complex assembly / CAK-ERCC2 complex / nuclear pore nuclear basket / UV protection / embryonic cleavage / DNA 5'-3' helicase / G protein-coupled receptor internalization / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / UV-damage excision repair / 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 / 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 / centriole replication / ATPase activator activity / intrinsic apoptotic signaling pathway by p53 class mediator / RNA Polymerase I Transcription Initiation / glial cell projection / protein localization to nucleus / hematopoietic stem cell differentiation / mRNA transport / embryonic organ development / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription by RNA polymerase I / transcription elongation by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / SUMOylation of DNA damage response and repair proteins / transcription-coupled nucleotide-excision repair / response to UV / DNA helicase activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / hormone-mediated signaling pathway / RNA Polymerase II Pre-transcription Events / extracellular matrix organization / centriole / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / insulin-like growth factor receptor signaling pathway / AURKA Activation by TPX2 / regulation of cytokinesis / 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 / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / cellular response to gamma radiation / DNA Damage Recognition in GG-NER / NoRC negatively regulates rRNA expression / base-excision repair / multicellular organism growth / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / G-protein beta/gamma-subunit complex binding / microtubule cytoskeleton organization
Similarity search - Function
XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / : ...XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain 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 / 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 / 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. / Putative DNA-binding domain superfamily / ATP-dependent RNA helicase DEAD-box, conserved site / 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 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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 complementing XP-A cells / General transcription factor IIH subunit 1 / Centrin-2 / 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: 3.9 Å
AuthorsKim J / Yang W
Funding support United States, Japan, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK075037 United States
Japan Society for the Promotion of Science (JSPS)JP16H06307 Japan
Japan Society for the Promotion of Science (JSPS)JP21H03598 Japan
CitationJournal: Nature / Year: 2023
Title: Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.
Authors: Jinseok Kim / Chia-Lung Li / Xuemin Chen / Yanxiang Cui / Filip M Golebiowski / Huaibin Wang / Fumio Hanaoka / Kaoru Sugasawa / Wei Yang /
Abstract: Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts. After initial recognition by XPC in global genome repair or a stalled RNA ...Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts. After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases. Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported. How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification.
History
DepositionAug 31, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27997.png

Downloads & links

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Map

FileDownload / File: emd_27997.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.872 Å		0.83 Å/pix.
x 384 pix.
= 319.872 Å		0.83 Å/pix.
x 384 pix.
= 319.872 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.0073601343 - 0.030616356
Average (Standard dev.)0.00023469262 (±0.0013648528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.872 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27997_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27997_half_map_2.map
Projections & Slices
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Sample components

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Entire : protein DNA complex

EntireName: protein DNA complex
Components
  • Complex: protein DNA complex
    • 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
    • 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: DNA repair protein complementing XP-C cells
    • Protein or peptide: Centrin-2
    • Protein or peptide: DNA repair protein complementing XP-A cells
    • DNA: DNA (Cy5)
    • DNA: DNA
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

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Supramolecule #1: protein DNA complex

SupramoleculeName: protein DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 610 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.404961 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KVDEYGAKDY RLQMPLKDDH TSRPLWVAPD GHIFLEAFSP VYKYAQDFLV AIAEPVCRPT HVHEYKLTAY SLYAAVSVGL QTSDITEYL RKLSKTGVPD GIMQFIKLCT VSYGKVKLVL KHNRYFVESC HPDVIQHLLQ DPVIRECRLR NSEGEATETV S FEVKQEMI ...String:
KVDEYGAKDY RLQMPLKDDH TSRPLWVAPD GHIFLEAFSP VYKYAQDFLV AIAEPVCRPT HVHEYKLTAY SLYAAVSVGL QTSDITEYL RKLSKTGVPD GIMQFIKLCT VSYGKVKLVL KHNRYFVESC HPDVIQHLLQ DPVIRECRLR NSEGEATETV S FEVKQEMI EELQKRCIHL EYPLLAEYDF RNDSVNPDIN IDLKPTAVLR PYQEKSLRKM FGNGRARSGV IVLPCGAGKS LV GVTAACT VRKRCLVLGN SAVSVEQWKA QFKMWSTIDD SQICRFTSDA KDKPIGCSVA ISTYSMLGHT TKRSWEAERV MEW LKTQEW GLMILDEVHT IPAKMFRRVL TIVQAHCKLG LTATLVREDD KIVDLNFLIG PKLYEANWME LQNNGYIAKV QCAE VWCPM SPEFYREYVA IKTKKRILLY TMNPNKFRAC QFLIKFHERR NDKIIVFADN VFALKEYAIR LNKPYIYGPT SQGER MQIL QNFKHNPKIN TIFISKVGDT SFDLPEANVL IQISSHGGSR RQEAQRLGRV LRYNAFFYSL VSQDTQEMAY STKRQR FLV DQGYSFKVIT KLAGMEEEDL AFSTKEEQQQ LLQKVLAATD

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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 / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.58225 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 RQMAQPFHR

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: 49.56993 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LEEKNRMLQE DPVLFQLYKD LVVSQVISAE EFWANRLNVN ATDSSSTSNH KQDVGISAAF LADVRPQTDG CNGLRYNLTS DIIESIFRT YPAVKMKYAE NVPHNMTEKE FWTRFFQSHY FHRDRLNTGS KDLFAECAKI DEKGLKTMVS LGVKNPLLDL T ALEDKPLD ...String:
LEEKNRMLQE DPVLFQLYKD LVVSQVISAE EFWANRLNVN ATDSSSTSNH KQDVGISAAF LADVRPQTDG CNGLRYNLTS DIIESIFRT YPAVKMKYAE NVPHNMTEKE FWTRFFQSHY FHRDRLNTGS KDLFAECAKI DEKGLKTMVS LGVKNPLLDL T ALEDKPLD EGYGISSVPS ASNSKSIKEN SNAAIIKRFN HHSAMVLAAG LRKQEAQNEQ TSEPSNMDGN SGDADCFQPA VK RAKLQES IEYEDLGKNN SVKTIALNLK KSDRYYHGPT PIQSLQYATS QDIINSFQSI RQEMEAYTPK LTQVLSSSAA SST ITALSP GGALMQGGTQ QAINQMVPND IQSELKHLYV AVGELLRHFW SCFPVNTPFL EEKVVKMKSN LERFQVTKLC PFQE KIRRQ YLSTNLVSHI EEMLQTAYNK LHTWQSRRLM KKT

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: 50.432066 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: RNLQEFLGGL SPGVLDRLYG HPATCLAVFR ELPSLAKNWV MRMLFLEQPL PQAAVALWVK KEFSKAQEES TGLLSGLRIW HTQLLPGGL QGLILNPIFR QNLRIALLGG GKAWSDDTSQ LGPDKHARDV PSLDKYAEER WEVVLHFMVG SPSAAVSQDL A QLLSQAGL ...String:
RNLQEFLGGL SPGVLDRLYG HPATCLAVFR ELPSLAKNWV MRMLFLEQPL PQAAVALWVK KEFSKAQEES TGLLSGLRIW HTQLLPGGL QGLILNPIFR QNLRIALLGG GKAWSDDTSQ LGPDKHARDV PSLDKYAEER WEVVLHFMVG SPSAAVSQDL A QLLSQAGL MKSTEPGEPP CITSAGFQFL LLDTPAQLWY FMLQYLQTAQ SRGMDLVEIL SFLFQLSFST LGKDYSVEGM SD SLLNFLQ HLREFGLVFQ RKRKSRRYYP TRLAINLSSG VSGAGGTVHQ PGFIVVETNY RLYAYTESEL QIALIALFSE MLY RFPNMV VAQVTRESVQ QAIASGITAQ QIIHFLRTRA HPVMLKQTPV LPPTITDQIR LWELERDRLR FTEGVLYNQF LSQV DFELL LAHARELGVL VFENSAKRLM VVTPAGHSDV KRFWKRQKHS S

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: 42.772086 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TKRWEGGYER TWEILKEDES GSLKATIEDI LFKAKRKRVF EHHGGVRLGM MRHLYVVVDG SRTMEDQDLK PNRLTCTLKL LEYFVEEYF DQNPISQIGI IVTKSKRAEK LTELSGNPRK HITSLKKAVD MTCHGEPSLY NSLSIAMQTL KHMPGHTSRE V LIIFSSLT ...String:
TKRWEGGYER TWEILKEDES GSLKATIEDI LFKAKRKRVF EHHGGVRLGM MRHLYVVVDG SRTMEDQDLK PNRLTCTLKL LEYFVEEYF DQNPISQIGI IVTKSKRAEK LTELSGNPRK HITSLKKAVD MTCHGEPSLY NSLSIAMQTL KHMPGHTSRE V LIIFSSLT TCDPSNIYDL IKTLKAAKIR VSVIGLSAEV RVCTVLARET GGTYHVILDE SHYKELLTHH VSPPPASSSS EC SLIRMGF PQHTIASLSD QDAKPSFSMA HLDGNTEPGL TLGGYFCPQC RAKYCELPVE CKICGLTLVS APHLARSYHH LFP LDAFQE IPLEEYNGER FCYGCQGELK DQHVYVCAVC QNVFCVDCDV FVHDSLHCCP GCIH

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: 31.788727 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DELNLLVIVV DANPIWWGKQ ALKESQFTLS KCIDAVMVLG NSHLFMNRSN KLAVIASHIQ ESRFLYPGKN GRLGDFFGDP GNPPEFNPS GSKDGKYELL TSANEVIVEE IKDLMTKSDI KGQHTETLLA GSLAKALCYI HRMNKEVKDN QEMKSRILVI K AAEDSALQ ...String:
DELNLLVIVV DANPIWWGKQ ALKESQFTLS KCIDAVMVLG NSHLFMNRSN KLAVIASHIQ ESRFLYPGKN GRLGDFFGDP GNPPEFNPS GSKDGKYELL TSANEVIVEE IKDLMTKSDI KGQHTETLLA GSLAKALCYI HRMNKEVKDN QEMKSRILVI K AAEDSALQ YMNFMNVIFA AQKQNILIDA CVLDSDSGLL QQACDITGGL YLKVPQMPSL LQYLLWVFLP DQDQRSQLIL PP PVHVDYR AACFCHRNLI EIGYVCSVCL SIFCNFSPIC TTCETAF

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: 7.458625 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
VLKGVLIECD PAMKQFLLYL DESNALGKKF IIQDIDDTHV FVIAELVNVL QERVGELMDQ NAFSLT

UniProtKB: General transcription factor IIH subunit 5

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Macromolecule #8: DNA repair protein complementing XP-C cells

MacromoleculeName: DNA repair protein complementing XP-C cells / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.55235 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: PTAIGLYKNH PLYALKRHLL KYEAIYPETA AILGYCRGEA VYSRDCVHTL HSRDTWLKKA RVVRLGEVPY KMVKGFSNRA RKARLAEPQ LREENDLGLF GYWQTEEYQP PVAVDGKVPR NEFGNVYLFL PSMMPIGCVQ LNLPNLHRVA RKLDIDCVQA I TGFDFHGG ...String:
PTAIGLYKNH PLYALKRHLL KYEAIYPETA AILGYCRGEA VYSRDCVHTL HSRDTWLKKA RVVRLGEVPY KMVKGFSNRA RKARLAEPQ LREENDLGLF GYWQTEEYQP PVAVDGKVPR NEFGNVYLFL PSMMPIGCVQ LNLPNLHRVA RKLDIDCVQA I TGFDFHGG YSHPVTDGYI VCEEFKDVLL TAWENEQAVI ERKEKEKKEK RALGNWKLLA KGLLIRERLK RRYGGTSSQA EA ARILAAS WPQNREDEEK QKEKKAAASH LFPFEKL

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Macromolecule #9: Centrin-2

MacromoleculeName: Centrin-2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.183146 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
KEEILKAFKL FDDDETGKIS FKNLKRVAKE LGENLTDEEL QEMIDEADRD GDGEVSEQEF LRIMKKTSLY

UniProtKB: Centrin-2

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Macromolecule #10: DNA repair protein complementing XP-A cells

MacromoleculeName: DNA repair protein complementing XP-A cells / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.787939 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
YVICEECGKE FMDSYLMNHF DLPTCDNCRD ADDKHKLITK TEAKQEYLLK DCDLEKREPP LKFIVKKNPH HSQWGDMKLY LKLQIVKRS LEVWGSQEAL EEAKEVRQEN REKMKQKKFD KKVKELRRAV RSSVWKRETI VHQHEYGPEE NLEDDMYRKT C TMCGHELT YEKM

UniProtKB: DNA repair protein complementing XP-A cells

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Macromolecule #11: DNA (Cy5)

MacromoleculeName: DNA (Cy5) / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.914215 KDa
SequenceString:
(DA)(DG)(DG)(DT)(DA)(DG)(DT)(DC)(DA)(DC) (DA)(DG)(DC)(DT)(DG)(DA)(DT)(DT)(DG)(DC) (DG)(DC)(DT)(DG)(DA)(DG)(DG)(DA)(DT) (VM6)(DT)(DA)(DG)(DA)(DC)(DG)(DT)(DG)(DC) (DG)(DA)(DT)(DA)(DT)

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Macromolecule #12: DNA

MacromoleculeName: DNA / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.707808 KDa
SequenceString:
(DA)(DT)(DA)(DT)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DC)(DT)(DA)(DT)(DT)(DA)(DT)(DC)(DC) (DT)(DC)(DA)(DG)(DC)(DG)(DC)(DA)(DA) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DT)(DG)(DA) (DC) (DT)(DA)(DC)(DC)(DT)

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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

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Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #15: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 15 / 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

Concentration0.4 mg/mL
BufferpH: 7.9
Component:
ConcentrationFormulaName
25.0 mMHEPES4-(2-Hydroxyethyl)-1-piperazine ethanesulfonic acid
100.0 mMKClPotassium Chloride
0.5 %GlycerolGlycerol
2.0 mMMgCl2Magnesium Chloride
2.0 mMTCEP(Tris(2-carboxyethyl)phospine)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6243 / Average exposure time: 2.5 sec. / Average electron dose: 54.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 105000
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: 1645921
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ro4

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 173440
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ro4


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: correlation coefficient
Output model

PDB-8ebt:
XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5)

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