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- EMDB-51680: Cryo_EM structure of human FAN1 R507H mutant in complex with 5' f... -

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Basic information

Entry
Database: EMDB / ID: EMD-51680
TitleCryo_EM structure of human FAN1 R507H mutant in complex with 5' flap DNA substrate and PCNA
Map data
Sample
  • Complex: Ternary complex of FAN1 R507H-PCNA-DNA
    • Complex: FAN1 R507H-PCNA
      • Protein or peptide: Fanconi-associated nuclease 1
      • Protein or peptide: Proliferating cell nuclear antigen
    • Complex: DNA
      • DNA: DNA (Continuous)
      • DNA: DNA (Pre-Nick)
      • DNA: DNA (Post-Nick)
  • Ligand: CALCIUM ION
KeywordsFAN1 R507H / PCNA / DNA BINDING PROTEIN
Function / homology
Function and homology information


flap-structured DNA binding / phosphodiesterase I / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / 5'-flap endonuclease activity / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity ...flap-structured DNA binding / phosphodiesterase I / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / 5'-flap endonuclease activity / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / ubiquitin-modified protein reader activity / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / 5'-3' exonuclease activity / phosphodiesterase I activity / response to dexamethasone / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / translesion synthesis / estrous cycle / interstrand cross-link repair / mismatch repair / intercellular bridge / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / liver regeneration / epithelial cell differentiation / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / positive regulation of DNA replication / nuclear estrogen receptor binding / male germ cell nucleus / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / chromatin organization / damaged DNA binding / chromosome, telomeric region / nuclear body / cilium / DNA repair / centrosome / chromatin binding / chromatin / protein-containing complex binding / enzyme binding / magnesium ion binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
: / : / : / Fanconi-associated nuclease 1, SAP subdomain / Fanconi-associated nuclease 1, TPR domain / Fanconi-associated nuclease 1-like / : / FAN1, HTH domain / VRR-NUC domain / VRR-NUC domain ...: / : / : / Fanconi-associated nuclease 1, SAP subdomain / Fanconi-associated nuclease 1, TPR domain / Fanconi-associated nuclease 1-like / : / FAN1, HTH domain / VRR-NUC domain / VRR-NUC domain / VRR_NUC / Rad18-like CCHC zinc finger / tRNA endonuclease-like domain superfamily / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / :
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Fanconi-associated nuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsJeyasankar G / Salerno-Kochan A / Thomsen M
Funding support United States, 1 items
OrganizationGrant numberCountry
CHDI Foundation United States
Citation
Journal: Nat Commun / Year: 2025
Title: A FAN1 point mutation associated with accelerated Huntington's disease progression alters its PCNA-mediated assembly on DNA.
Authors: Jonas Aretz / Gayathri Jeyasankar / Anna Salerno-Kochan / Maren Thomsen / Gabriel Thieulin-Pardo / Tasir Haque / Edith Monteagudo / Dan Felsenfeld / Michael Finley / Thomas F Vogt / Julien ...Authors: Jonas Aretz / Gayathri Jeyasankar / Anna Salerno-Kochan / Maren Thomsen / Gabriel Thieulin-Pardo / Tasir Haque / Edith Monteagudo / Dan Felsenfeld / Michael Finley / Thomas F Vogt / Julien Boudet / Brinda C Prasad /
Abstract: FAN1 is an endo- and exo-nuclease involved in DNA and interstrand crosslink repair. Genome-wide association studies of people with Huntington's disease revealed a strong association between the FAN1 ...FAN1 is an endo- and exo-nuclease involved in DNA and interstrand crosslink repair. Genome-wide association studies of people with Huntington's disease revealed a strong association between the FAN1 R507H mutation and early disease onset, however the underlying mechanism(s) remains unclear. FAN1 has previously been implicated in modulating triplet repeat expansion in a PCNA dependent manner. To examine the role of PCNA on FAN1 activation, we solved the cryo-EM structures of a PCNA-FAN1-DNA complex. Our findings reveal that the FAN1 R507 residue directly interacts with PCNA D232. Biophysical interaction studies demonstrated that FAN1 enhances the binding affinity of PCNA for DNA, a synergistic effect disrupted in mutants carrying the R507H mutation. In contrast, PCNA does not affect the affinity of FAN1 for DNA but does modulate FAN1 activity upon ternary complex formation. The weakened and functionally altered FAN1 R507H-PCNA-DNA complex may partly impair the FAN1-mediated repair of CAG extrahelical extrusions, providing a potential explanation for the mutation's role in accelerating disease progression.
#1: Journal: Biorxiv / Year: 2024
Title: A FAN1 point mutation associated with accelerated Huntington's disease progression alters its PCNA-mediated assembly on DNA
Authors: Aretz J / Jeyasankar G / Salerno-Kochan A / Thomsen M / Thieulin-Pardo G / Haque T / Monteagudo E / Felsenfeld D / Finley M / Vogt TF / Boudet J / Prasad BC
History
DepositionOct 1, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51680.png

Downloads & links

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Map

FileDownload / File: emd_51680.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 300 pix.
= 274.26 Å		0.91 Å/pix.
x 300 pix.
= 274.26 Å		0.91 Å/pix.
x 300 pix.
= 274.26 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9142 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-2.0853915 - 3.2395957
Average (Standard dev.)-0.0007906135 (±0.057534613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 274.26 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51680_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_51680_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of FAN1 R507H-PCNA-DNA

EntireName: Ternary complex of FAN1 R507H-PCNA-DNA
Components
  • Complex: Ternary complex of FAN1 R507H-PCNA-DNA
    • Complex: FAN1 R507H-PCNA
      • Protein or peptide: Fanconi-associated nuclease 1
      • Protein or peptide: Proliferating cell nuclear antigen
    • Complex: DNA
      • DNA: DNA (Continuous)
      • DNA: DNA (Pre-Nick)
      • DNA: DNA (Post-Nick)
  • Ligand: CALCIUM ION

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Supramolecule #1: Ternary complex of FAN1 R507H-PCNA-DNA

SupramoleculeName: Ternary complex of FAN1 R507H-PCNA-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: FAN1 R507H-PCNA

SupramoleculeName: FAN1 R507H-PCNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fanconi-associated nuclease 1

MacromoleculeName: Fanconi-associated nuclease 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 114.705156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPMGMMSEGK PPDKKRPRRS LSISKNKKKA SNSIISCFNN APPAKLACPV CSKMVPRYDL NRHLDEMCAN NDFVQVDPGQ VGLINSNVS MVDLTSVTLE DVTPKKSPPP KTNLTPGQSD SAKREVKQKI SPYFKSNDVV CKNQDELRNR SVKVICLGSL A SKLSRKYV ...String:
GPMGMMSEGK PPDKKRPRRS LSISKNKKKA SNSIISCFNN APPAKLACPV CSKMVPRYDL NRHLDEMCAN NDFVQVDPGQ VGLINSNVS MVDLTSVTLE DVTPKKSPPP KTNLTPGQSD SAKREVKQKI SPYFKSNDVV CKNQDELRNR SVKVICLGSL A SKLSRKYV KAKKSIDKDE EFAGSSPQSS KSTVVKSLID NSSEIEDEDQ ILENSSQKEN VFKCDSLKEE CIPEHMVRGS KI MEAESQK ATRECEKSAL TPGFSDNAIM LFSPDFTLRN TLKSTSEDSL VKQECIKEVV EKREACHCEE VKMTVASEAK IQL SDSEAK SHSSADDASA WSNIQEAPLQ DDSCLNNDIP HSIPLEQGSS CNGPGQTTGH PYYLRSFLVV LKTVLENEDD MLLF DEQEK GIVTKFYQLS ATGQKLYVRL FQRKLSWIKM TKLEYEEIAL DLTPVIEELT NAGFLQTESE LQELSEVLEL LSAPE LKSL AKTFHLVNPN GQKQQLVDAF LKLAKQHSVC TWGKNKPGIG AVILKRAKAL AGQSVRICKG PRAVFSRILL LFSLTD SME DEDAACGGQG QLSTVLLVNL GRMEFPSYTI NRKTHIFQDR DDLIRYAAAT HMLSDISSAM ANGNWEEAKE LAQCAKR DW NRLKNHPSLR CHEDLPLFLR CFTVGWIYTR ILSRFVEILQ RLHMYEEAVR ELESLLSQRI YCPDSRGRWW DRLALNLH Q HLKRLEPTIK CITEGLADPE VRTGHRLSLY QRAVRLRESP SCKKFKHLFQ QLPEMAVQDV KHVTITGRLC PQRGMCKSV FVMEAGEAAD PTTVLCSVEE LALAHYRRSG FDQGIHGEGS TFSTLYGLLL WDIIFMDGIP DVFRNACQAF PLDLCTDSFF TSRRPALEA RLQLIHDAPE ESLRAWVAAT WHEQEGRVAS LVSWDRFTSL QQAQDLVSCL GGPVLSGVCR HLAADFRHCR G GLPDLVVW NSQSRHFKLV EVKGPNDRLS HKQMIWLAEL QKLGAEVEVC HVVAVGAKSQ SLS

UniProtKB: Fanconi-associated nuclease 1

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Macromolecule #5: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.949912 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPMFEARLVQ GSILKKVLEA LKDLINEACW DISSSGVNLQ SMDSSHVSLV QLTLRSEGFD TYRCDRNLAM GVNLTSMSKI LKCAGNEDI ITLRAEDNAD TLALVFEAPN QEKVSDYEMK LMDLDVEQLG IPEQEYSCVV KMPSGEFARI CRDLSHIGDA V VISCAKDG ...String:
GPMFEARLVQ GSILKKVLEA LKDLINEACW DISSSGVNLQ SMDSSHVSLV QLTLRSEGFD TYRCDRNLAM GVNLTSMSKI LKCAGNEDI ITLRAEDNAD TLALVFEAPN QEKVSDYEMK LMDLDVEQLG IPEQEYSCVV KMPSGEFARI CRDLSHIGDA V VISCAKDG VKFSASGELG NGNIKLSQTS NVDKEEEAVT IEMNEPVQLT FALRYLNFFT KATPLSSTVT LSMSADVPLV VE YKIADMG HLKYYLAPKI EDEEGS

UniProtKB: Proliferating cell nuclear antigen

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Macromolecule #2: DNA (Continuous)

MacromoleculeName: DNA (Continuous) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.15474 KDa
SequenceString:
(DC)(DC)(DC)(DG)(DT)(DC)(DC)(DA)(DG)(DG) (DT)(DC)(DT)(DC)(DG)(DT)(DC)(DC)(DG)(DC) (DG)(DC)(DC)(DA)(DC)(DT)(DC)(DG)(DT) (DG)(DT)(DC)(DC)(DA)(DG)(DC)(DG)(DT)(DC) (DG)

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Macromolecule #3: DNA (Pre-Nick)

MacromoleculeName: DNA (Pre-Nick) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.618535 KDa
SequenceString:
(DC)(DG)(DA)(DC)(DG)(DC)(DT)(DG)(DG)(DA) (DC)(DA)(DC)(DG)(DA)(DG)(DT)(DG)(DG)(DC) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #4: DNA (Post-Nick)

MacromoleculeName: DNA (Post-Nick) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.554223 KDa
SequenceString:
(DT)(DG)(DC)(DG)(DG)(DA)(DC)(DG)(DA)(DG) (DA)(DC)(DC)(DT)(DG)(DG)(DA)(DC)(DG)(DG) (DG)

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 1 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 487606
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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