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- EMDB-29673: Bulky DNA lesion recognition complex 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-29673
TitleBulky DNA lesion recognition complex 3
Map data
Sample
  • Complex: bulky DNA lesion recognition complex 3
    • Protein or peptide: x 9 types
    • DNA: x 2 types
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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
DepositionFeb 2, 2023-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29673.png

Downloads & links

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Map

FileDownload / File: emd_29673.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.833 Å
Density
Contour LevelBy AUTHOR: 0.0055
Minimum - Maximum-0.011614569 - 0.035504956
Average (Standard dev.)0.00012301131 (±0.0010382026)
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_29673_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_29673_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : bulky DNA lesion recognition complex 3

EntireName: bulky DNA lesion recognition complex 3
Components
  • Complex: bulky DNA lesion recognition complex 3
    • 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: DNA repair protein complementing XP-C cells
    • Protein or peptide: DNA repair protein complementing XP-A cells
    • DNA: DNA1
    • DNA: DNA2

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Supramolecule #1: bulky DNA lesion recognition complex 3

SupramoleculeName: bulky DNA lesion recognition complex 3 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 440 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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: mgkrdradrd kkksrkrhye deeddeedap gndpqeavps aagkqvdesg tkvdeygakd yrlqmplkd dhtsrplwva pdghifleaf spvykyaqdf lvaiaepvcr pthvheyklt a yslyaavs vglqtsdite ylrklsktgv pdgimqfikl ctvsygkvkl ...String:
mgkrdradrd kkksrkrhye deeddeedap gndpqeavps aagkqvdesg tkvdeygakd yrlqmplkd dhtsrplwva pdghifleaf spvykyaqdf lvaiaepvcr pthvheyklt a yslyaavs vglqtsdite ylrklsktgv pdgimqfikl ctvsygkvkl vlkhnryfve sc hpdviqh llqdpvirec rlrnsegeat elitetftsk saisktaess ggpstsrvtd pqg ksdipm dlfdfyeqmd kdeeeeeetq tvsfevkqem ieelqkrcih leypllaeyd frnd svnpd inidlkptav lrpyqekslr kmfgngrars gvivlpcgag kslvgvtaac tvrkr clvl gnsavsveqw kaqfkmwsti ddsqicrfts dakdkpigcs vaistysmlg httkrs wea ervmewlktq ewglmildev htipakmfrr vltivqahck lgltatlvre ddkivdl nf ligpklyean wmelqnngyi akvqcaevwc pmspefyrey vaiktkkril lytmnpnk f racqflikfh errndkiivf adnvfalkey airlnkpyiy gptsqgermq ilqnfkhnp kintifiskv gdtsfdlpea nvliqisshg gsrrqeaqrl grvlrakkgm vaeeynaffy slvsqdtqe maystkrqrf lvdqgysfkv itklagmeee dlafstkeeq qqllqkvlaa t dldaeeev vagefgsrss qasrrfgtms smsgaddtvy meyhssrska pskhvhplfk rf rk

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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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: mklnvdgllv yfpydyiype qfsymrelkr tldakghgvl empsgtgktv sllalimayq rayplevtk liycsrtvpe iekvieelrk llnfyekqeg eklpflglal ssrknlcihp e vtplrfgk dvdgkchslt asyvraqyqh dtslphcrfy eefdahgrev ...String:
mklnvdgllv yfpydyiype qfsymrelkr tldakghgvl empsgtgktv sllalimayq rayplevtk liycsrtvpe iekvieelrk llnfyekqeg eklpflglal ssrknlcihp e vtplrfgk dvdgkchslt asyvraqyqh dtslphcrfy eefdahgrev plpagiynld dl kalgrrq gwcpyflary silhanvvvy syhylldpki adlvskelar kavvvfdeah nid nvcids msvnltrrtl drcqgnletl qktvlriket deqrlrdeyr rlveglreas aare tdahl anpvlpdevl qeavpgsirt aehflgflrr lleyvkwrlr vqhvvqespp aflsg laqr vciqrkplrf caerlrsllh tleitdladf spltllanfa tlvstyakgf tiiiep fdd rtptianpil hfscmdasla ikpvferfqs viitsgtlsp ldiypkildf hpvtmat ft mtlarvclcp miigrgndqv aisskfetre diavirnygn lllemsavvp dgivafft s yqymestvas wyeqgileni qrnkllfiet qdgaetsval ekyqeaceng rgaillsva rgkvsegidf vhhygravim fgvpyvytqs rilkarleyl rdqfqirend fltfdamrha aqcvgrair gktdyglmvf adkrfargdk rgklprwiqe hltdanlnlt vdegvqvaky f lrqmaqpf hredqlglsl lsleqlesee tlkrieqiaq qlDYKDDDDK

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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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: matsseevll ivkkvrqkkq dgalylmaer iawapegkdr ftishmyadi kcqkispegk akiqlqlvl hagdttnfhf snestavker davkdllqql lpkfkrkank eleeknrmlq e dpvlfqly kdlvvsqvis aeefwanrln vnatdsssts nhkqdvgisa ...String:
matsseevll ivkkvrqkkq dgalylmaer iawapegkdr ftishmyadi kcqkispegk akiqlqlvl hagdttnfhf snestavker davkdllqql lpkfkrkank eleeknrmlq e dpvlfqly kdlvvsqvis aeefwanrln vnatdsssts nhkqdvgisa afladvrpqt dg cnglryn ltsdiiesif rtypavkmky aenvphnmte kefwtrffqs hyfhrdrlnt gsk dlfaec akidekglkt mvslgvknpl ldltaledkp ldegygissv psasnsksik ensn aaiik rfnhhsamvl aaglrkqeaq neqtsepsnm dgnsgdadcf qpavkraklq esiey edlg knnsvktial nlkksdryyh gptpiqslqy atsqdiinsf qsirqemeay tpkltq vls ssaasstita lspggalmqg gtqqainqmv pndiqselkh lyvavgellr hfwscfp vn tpfleekvvk mksnlerfqv tklcpfqeki rrqylstnlv shieemlqta ynklhtwq s rrlmkkt

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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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: mestpsrgln rvhlqcrnlq eflgglspgv ldrlyghpat clavfrelps laknwvmrml fleqplpqa avalwvkkef skaqeestgl lsglriwhtq llpgglqgli lnpifrqnlr i allgggka wsddtsqlgp dkhardvpsl dkyaeerwev vlhfmvgsps ...String:
mestpsrgln rvhlqcrnlq eflgglspgv ldrlyghpat clavfrelps laknwvmrml fleqplpqa avalwvkkef skaqeestgl lsglriwhtq llpgglqgli lnpifrqnlr i allgggka wsddtsqlgp dkhardvpsl dkyaeerwev vlhfmvgsps aavsqdlaql ls qaglmks tepgeppcit sagfqfllld tpaqlwyfml qylqtaqsrg mdlveilsfl fql sfstlg kdysvegmsd sllnflqhlr efglvfqrkr ksrryyptrl ainlssgvsg aggt vhqpg fivvetnyrl yayteselqi alialfseml yrfpnmvvaq vtresvqqai asgit aqqi ihflrtrahp vmlkqtpvlp ptitdqirlw elerdrlrft egvlynqfls qvdfel lla harelgvlvf ensakrlmvv tpaghsdvkr fwkrqkhss

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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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SSGLEVLFQG PHMDEEPERT KRWEGGYERT WEILKEDESG SLKATIEDIL FKAKRKRVFE HHGQVRLGMM RHLYVVVDGS RTMEDQDLKP NRLTCTLKLL EYFVEEYFDQ NPISQIGIIV TKSKRAEKLT ELSGNPRKHI TSLKKAVDMT CHGEPSLYNS ...String:
MGSSHHHHHH SSGLEVLFQG PHMDEEPERT KRWEGGYERT WEILKEDESG SLKATIEDIL FKAKRKRVFE HHGQVRLGMM RHLYVVVDGS RTMEDQDLKP NRLTCTLKLL EYFVEEYFDQ NPISQIGIIV TKSKRAEKLT ELSGNPRKHI TSLKKAVDMT CHGEPSLYNS LSIAMQTLKH MPGHTSREVL IIFSSLTTCD PSNIYDLIKT LKAAKIRVSV IGLSAEVRVC TVLARETGGT YHVILDESHY KELLTHHVSP PPASSSSECS LIRMGFPQHT IASLSDQDAK PSFSMAHLDG NTEPGLTLGG YFCPQCRAKY CELPVECKIC GLTLVSAPHL ARSYHHLFPL DAFQEIPLEE YNGERFCYGC QGELKDQHVY VCAVCQNVFC VDCDVFVHDS LHCCPGCIHK IPAPSGV

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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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: mvsdedelnl lvivvdanpi wwgkqalkes qftlskcida vmvlgnshlf mnrsnklavi ashiqesrf lypgkngrlg dffgdpgnpp efnpsgskdg kyelltsane viveeikdlm t ksdikgqh tetllagsla kalcyihrmn kevkdnqemk srilvikaae ...String:
mvsdedelnl lvivvdanpi wwgkqalkes qftlskcida vmvlgnshlf mnrsnklavi ashiqesrf lypgkngrlg dffgdpgnpp efnpsgskdg kyelltsane viveeikdlm t ksdikgqh tetllagsla kalcyihrmn kevkdnqemk srilvikaae dsalqymnfm nv ifaaqkq nilidacvld sdsgllqqac ditgglylkv pqmpsllqyl lwvflpdqdq rsq lilppp vhvdyraacf chrnlieigy vcsvclsifc nfspicttce tafkislppv lkak kkklk vsa

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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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
mvnvlkgvli ecdpamkqfl lyldesnalg kkfiiqdidd thvfviaelv nvlqervgel mdqnafslt qk

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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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: M D Y K D D D D K H M A R K R A A G G E P R G R E L R S Q K S K A K S K A R R E E E E E D A F E D E K P P K K S L L S K V S Q G K R K R G C S H P G G S A D G P A K K K V A K ...String:
M D Y K D D D D K H M A R K R A A G G E P R G R E L R S Q K S K A K S K A R R E E E E E D A F E D E K P P K K S L L S K V S Q G K R K R G C S H P G G S A D G P A K K K V A K V T V K S E N L K V I K D E A L S D G D D L R D F P S D L K K A H H L K R G A T M N E D S N E E E E E S E N D W E E V E E L S E P V L G D V R E S T A F S R S L L P V K P V E I E I E T P E Q A K T R E R S E K I K L E F E T Y L R R A M K R F N K G V H E D T H K V H L L C L L A N G F Y R N N I C S Q P D L H A I G L S I I P A R F T R V L P R D V D T Y Y L S N L V K W F I G T F T V N A E L S A S E Q D N L Q T T L E R R F A I Y S A R D D E E L V H I F L L I L R A L Q L L T R L V L S L Q P I P L K S A T A K G K K P S K E R L T A D P G G S S E T S S Q V L E N H T K P K T S K G T K Q E E T F A K G T C R P S A K G K R N K G G R K K R S K P S S S E E D E G P G D K Q E K A T Q R R P H G R E R R V A S R V S Y K E E S G S D E A G S G S D F E L S S G E A S D P S D E D S E P G P P K Q R K A P A P Q R T K A G S K S A S R T H R G S H R K D P S L P V A S S S S S S S K R G K K M C S D G E K A E K R S I A G I D Q W L E V F C E Q E E K W V C V D C V H G V V G Q P L T C Y K Y A T K P M T Y V V G I D S D G W V R D V T Q R Y D P V W M T V T R K C R V D A E W W A E T L R P Y Q S P F M D R E K K E D L E F Q A K H M D Q P L P T A I G L Y K N H P L Y A L K R H L L K Y E A I Y P E T A A I L G Y C R G E A V Y S R D C V H T L H S R D T W L K K A R V V R L G E V P Y K M V K G F S N R A R K A R L A E P Q L R E E N D L G L F G Y W Q T E E Y Q P P V A V D G K V P R N E F G N V Y L F L P S M M P I G C V Q L N L P N L H R V A R K L D I D C V Q A I T G F D F H G G Y S H P V T D G Y I V C E E F K D V L L T A W E N E Q A V I E R K E K E K K E K R A L G N W K L L A K G L L I R E R L K R R Y G P K S E A A A P H T D A G G G L S S D E E E G T S S Q A E A A R I L A A S W P Q N R E D E E K Q K L K G G P K K T K R E K K A A A S H L F P F E K L

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Macromolecule #9: DNA repair protein complementing XP-A cells

MacromoleculeName: DNA repair protein complementing XP-A cells / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: maaadgalpe aaaleqpael pasvrasier krqralmlrq arlaarpysa taaaatggma nvkaapkii dtgggfilee eeeeeqkigk vvhqpgpvme fdyviceecg kefmdsylmn h fdlptcdn crdaddkhkl itkteakqey llkdcdlekr epplkfivkk ...String:
maaadgalpe aaaleqpael pasvrasier krqralmlrq arlaarpysa taaaatggma nvkaapkii dtgggfilee eeeeeqkigk vvhqpgpvme fdyviceecg kefmdsylmn h fdlptcdn crdaddkhkl itkteakqey llkdcdlekr epplkfivkk nphhsqwgdm kl ylklqiv krslevwgsq ealeeakevr qenrekmkqk kfdkkvkelr ravrssvwkr eti vhqhey gpeenleddm yrktctmcgh eltyekm

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Macromolecule #10: DNA1

MacromoleculeName: DNA1 / type: dna / ID: 10 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
AGGTAGTCAC AGCTGATTGC GCTGAGGAT(Cy5) TAGACGTGCG ATATCTATGC CA

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Macromolecule #11: DNA2

MacromoleculeName: DNA2 / type: dna / ID: 11 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
TGGCATAGAT ATCGCACGTC TATTATCCTC AGCGCAATCA GCTGTGACTA CCT

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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:
ConcentrationNameFormula
25.0 mM4-(2-Hydroxyethyl)-1-piperazine ethanesulfonic acid
100.0 mMpotassium chlorideKCl
0.5 %Glycerol
2.0 mMMagnesium chlorideMgCl2
2.0 mM(Tris(2-carboxyethyl)phospine)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
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: 105000
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: 6243 / 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: 5439765
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ro4

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 177287
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient

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