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- EMDB-28000: Initial DNA-lesion (AP) binding by XPC and TFIIH complex2 -

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Basic information

Entry
Database: EMDB / ID: EMD-28000
TitleInitial DNA-lesion (AP) binding by XPC and TFIIH complex2
Map data
Sample
  • Complex: small DNA lesion recognition complex2
    • Protein or peptide: x 10 types
    • DNA: x 2 types
  • Ligand: x 3 types
Function / homology
Function and homology information


XPC complex / 9+2 motile cilium / 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 / heterotrimeric G-protein binding / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly ...XPC complex / 9+2 motile cilium / 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 / heterotrimeric G-protein binding / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / transcription export complex 2 / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / nuclear pore nuclear basket / UV protection / CAK-ERCC2 complex / embryonic cleavage / 5'-3' DNA helicase activity / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cellular response to interleukin-7 / 3'-5' DNA helicase activity / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / spinal cord development / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / proteasome binding / 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 / erythrocyte maturation / regulation of cyclin-dependent protein serine/threonine kinase activity / ATPase activator activity / RNA Polymerase I Transcription Initiation / centriole replication / transcription elongation by RNA polymerase I / DNA topological change / polyubiquitin modification-dependent protein binding / intrinsic apoptotic signaling pathway by p53 class mediator / transcription-coupled nucleotide-excision repair / mRNA transport / hematopoietic stem cell differentiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / transcription by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / SUMOylation of DNA damage response and repair proteins / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to UV / 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 / RNA Polymerase II Pre-transcription Events / Anchoring of the basal body to the plasma membrane / DNA helicase activity / centriole / hormone-mediated signaling pathway / extracellular matrix organization / proteasome complex / AURKA Activation by TPX2 / Josephin domain DUBs / post-embryonic development / insulin-like growth factor receptor signaling pathway / ciliary basal body / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of cytokinesis / ubiquitin binding / chromosome segregation / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / determination of adult lifespan / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / DNA Damage Recognition in GG-NER
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 / 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 / UBA/TS-N domain / Ubiquitin associated domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / ATP-dependent RNA helicase DEAD-box, conserved site / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / UBA-like superfamily / 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 / Papain-like cysteine peptidase superfamily / 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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / EF-hand domain pair / helicase superfamily c-terminal domain / Ubiquitin domain profile. / 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
Similarity search - Domain/homology
Xeroderma pigmentosum, complementation group C, isoform CRA_a / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIH subunit 1 / Centrin-2 / UV excision repair protein RAD23 homolog B / 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: 5.6 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-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28000.png

Downloads & links

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Map

FileDownload / File: emd_28000.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.245 Å
Density
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.028266052 - 0.042314656
Average (Standard dev.)4.530532e-05 (±0.0011368012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 373.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28000_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28000_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : small DNA lesion recognition complex2

EntireName: small DNA lesion recognition complex2
Components
  • Complex: small DNA lesion recognition complex2
    • Protein or peptide: TFIIH basal transcription factor complex helicase XPB subunit
    • 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, p52
    • 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: Xeroderma pigmentosum, complementation group C, isoform CRA_a
    • Protein or peptide: UV excision repair protein RAD23 homolog B
    • Protein or peptide: Centrin-2
    • DNA: DNA (Ap)
    • DNA: DNA
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: ZINC ION
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: small DNA lesion recognition complex2

SupramoleculeName: small DNA lesion recognition complex2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 580 KDa

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

MacromoleculeName: TFIIH basal transcription factor complex helicase XPB 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: 89.404734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

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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: 88.018047 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 RIEQIAQQLD YKDDDDK

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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: 62.116492 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 MKKT

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

MacromoleculeName: General transcription factor IIH subunit 4, p52 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.245156 KDa
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

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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: 46.926648 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SSGLEVLFQG PHMDEEPERT KRWEGGYERT WEILKEDESG SLKATIEDIL FKAKRKRVFE HHGQVRLGMM RHLYVVVDG SRTMEDQDLK PNRLTCTLKL LEYFVEEYFD QNPISQIGII VTKSKRAEKL TELSGNPRKH ITSLKKAVDM T CHGEPSLY ...String:
MGSSHHHHHH SSGLEVLFQG PHMDEEPERT KRWEGGYERT WEILKEDESG SLKATIEDIL FKAKRKRVFE HHGQVRLGMM RHLYVVVDG SRTMEDQDLK PNRLTCTLKL LEYFVEEYFD QNPISQIGII VTKSKRAEKL TELSGNPRKH ITSLKKAVDM T CHGEPSLY NSLSIAMQTL KHMPGHTSRE VLIIFSSLTT CDPSNIYDLI KTLKAAKIRV SVIGLSAEVR VCTVLARETG GT YHVILDE SHYKELLTHH VSPPPASSSS ECSLIRMGFP QHTIASLSDQ DAKPSFSMAH LDGNTEPGLT LGGYFCPQCR AKY CELPVE CKICGLTLVS APHLARSYHH LFPLDAFQEI PLEEYNGERF CYGCQGELKD QHVYVCAVCQ NVFCVDCDVF VHDS LHCCP GCIHKIPAPS GV

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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

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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

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Macromolecule #8: Xeroderma pigmentosum, complementation group C, isoform CRA_a

MacromoleculeName: Xeroderma pigmentosum, complementation group C, isoform CRA_a
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 107.437633 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKH MARKRAAGGE PRGRELRSQK SKAKSKARRE EEEEDAFEDE KPPKKSLLSK VSQGKRKRGC SHPGGSADGP AKKKVAKVT VKSENLKVIK DEALSDGDDL RDFPSDLKKA HHLKRGATMN EDSNEEEEES ENDWEEVEEL SEPVLGDVRE S TAFSRSLL ...String:
MDYKDDDDKH MARKRAAGGE PRGRELRSQK SKAKSKARRE EEEEDAFEDE KPPKKSLLSK VSQGKRKRGC SHPGGSADGP AKKKVAKVT VKSENLKVIK DEALSDGDDL RDFPSDLKKA HHLKRGATMN EDSNEEEEES ENDWEEVEEL SEPVLGDVRE S TAFSRSLL PVKPVEIEIE TPEQAKTRER SEKIKLEFET YLRRAMKRFN KGVHEDTHKV HLLCLLANGF YRNNICSQPD LH AIGLSII PARFTRVLPR DVDTYYLSNL VKWFIGTFTV NAELSASEQD NLQTTLERRF AIYSARDDEE LVHIFLLILR ALQ LLTRLV LSLQPIPLKS ATAKGKKPSK ERLTADPGGS SETSSQVLEN HTKPKTSKGT KQEETFAKGT CRPSAKGKRN KGGR KKRSK PSSSEEDEGP GDKQEKATQR RPHGRERRVA SRVSYKEESG SDEAGSGSDF ELSSGEASDP SDEDSEPGPP KQRKA PAPQ RTKAGSKSAS RTHRGSHRKD PSLPVASSSS SSSKRGKKMC SDGEKAEKRS IAGIDQWLEV FCEQEEKWVC VDCVHG VVG QPLTCYKYAT KPMTYVVGID SDGWVRDVTQ RYDPVWMTVT RKCRVDAEWW AETLRPYQSP FMDREKKEDL EFQAKHM DQ PLPTAIGLYK NHPLYALKRH LLKYEAIYPE TAAILGYCRG EAVYSRDCVH TLHSRDTWLK KARVVRLGEV PYKMVKGF S NRARKARLAE PQLREENDLG LFGYWQTEEY QPPVAVDGKV PRNEFGNVYL FLPSMMPIGC VQLNLPNLHR VARKLDIDC VQAITGFDFH GGYSHPVTDG YIVCEEFKDV LLTAWENEQA VIERKEKEKK EKRALGNWKL LAKGLLIRER LKRRYGPKSE AAAPHTDAG GGLSSDEEEG TSSQAEAARI LAASWPQNRE DEEKQKLKGG PKKTKREKKA AASHLFPFEK L

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Macromolecule #9: UV excision repair protein RAD23 homolog B

MacromoleculeName: UV excision repair protein RAD23 homolog B / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.275055 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 FDEDLEHHHH HH

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Macromolecule #10: Centrin-2

MacromoleculeName: Centrin-2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.769486 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MASNFKKANM ASSSQRKRMS PKPELTEEQK QEIREAFDLF DADGTGTIDV KELKVAMRAL GFEPKKEEIK KMISEIDKEG TGKMNFGDF LTVMTQKMSE KDTKEEILKA FKLFDDDETG KISFKNLKRV AKELGENLTD EELQEMIDEA DRDGDGEVSE Q EFLRIMKK TSLY

+
Macromolecule #11: DNA (Ap)

MacromoleculeName: DNA (Ap) / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 16.171333 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) (3DR)(3DR)(DT)(DA)(DG)(DA)(DC)(DG)(DT)(DG) (DC)(DG)(DA)(DT)(DA)(DT)(DC) ...String:
(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) (3DR)(3DR)(DT)(DA)(DG)(DA)(DC)(DG)(DT)(DG) (DC)(DG)(DA)(DT)(DA)(DT)(DC)(DT)(DA) (DT)(DG)(DC)(DC)(DA)

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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: 16.219405 KDa
SequenceString: (DT)(DG)(DG)(DC)(DA)(DT)(DA)(DG)(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) ...String:
(DT)(DG)(DG)(DC)(DA)(DT)(DA)(DG)(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 / Iron–sulfur cluster

+
Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 103000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3883 / Average exposure time: 2.5 sec. / Average electron dose: 54.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1145832
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Avg.num./class: 70000 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 66841
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6nmi

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8ebw:
Initial DNA-lesion (AP) binding by XPC and TFIIH complex2

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