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- EMDB-45664: Cryo-EM structure of FAN1-PCNA-DNA in final state -

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Basic information

Entry
Database: EMDB / ID: EMD-45664
TitleCryo-EM structure of FAN1-PCNA-DNA in final state
Map data
Sample
  • Complex: Ternary complex of FAN1-PCNA-DNA in final state
    • DNA: DNA (46-MER) with (CAG)2 extrusion
    • DNA: DNA (40-MER)
    • Protein or peptide: Proliferating cell nuclear antigen
    • Protein or peptide: Fanconi-associated nuclease 1
Keywordsnuclease / CAG expansion / DNA repair / Huntington's disease / DNA BINDING PROTEIN / PROTEIN BINDING
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 / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding / 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 / Removal of the Flap Intermediate from the C-strand / 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 / replisome / 5'-3' exonuclease activity / phosphodiesterase I activity / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / translesion synthesis / mismatch repair / interstrand cross-link repair / intercellular bridge / response to cadmium ion / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / male germ cell nucleus / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / liver regeneration / Translesion synthesis by POLI / replication fork / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / nuclear estrogen receptor binding / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / damaged DNA binding / chromosome, telomeric region / nuclear body / cilium / DNA repair / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsFenglin L / Anna P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of FAN1-PCNA-DNA in final state
Authors: Fenglin L / Anna P
History
DepositionJul 10, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45664.png

Downloads & links

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Map

FileDownload / File: emd_45664.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.21617506 - 0.47618592
Average (Standard dev.)0.00032916854 (±0.014848383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45664_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_45664_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 : Ternary complex of FAN1-PCNA-DNA in final state

EntireName: Ternary complex of FAN1-PCNA-DNA in final state
Components
  • Complex: Ternary complex of FAN1-PCNA-DNA in final state
    • DNA: DNA (46-MER) with (CAG)2 extrusion
    • DNA: DNA (40-MER)
    • Protein or peptide: Proliferating cell nuclear antigen
    • Protein or peptide: Fanconi-associated nuclease 1

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Supramolecule #1: Ternary complex of FAN1-PCNA-DNA in final state

SupramoleculeName: Ternary complex of FAN1-PCNA-DNA in final state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA (46-MER) with (CAG)2 extrusion

MacromoleculeName: DNA (46-MER) with (CAG)2 extrusion / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.231137 KDa
SequenceString:
(DC)(DG)(DA)(DA)(DT)(DT)(DT)(DC)(DT)(DA) (DG)(DA)(DC)(DT)(DC)(DG)(DA)(DG)(DA)(DT) (DC)(DA)(DG)(DC)(DA)(DG)(DC)(DT)(DG) (DC)(DT)(DA)(DG)(DG)(DT)(DC)(DG)(DA)(DG) (DT) (DC)(DT)(DA)(DG)(DA)(DG)

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Macromolecule #2: DNA (40-MER)

MacromoleculeName: DNA (40-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.25689 KDa
SequenceString:
(DC)(DT)(DC)(DT)(DA)(DG)(DA)(DC)(DT)(DC) (DG)(DA)(DC)(DC)(DT)(DA)(DG)(DC)(DA)(DG) (DA)(DT)(DC)(DT)(DC)(DG)(DA)(DG)(DT) (DC)(DT)(DA)(DG)(DA)(DA)(DA)(DT)(DT)(DC) (DG)

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Macromolecule #3: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.795752 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFEARLVQGS ILKKVLEALK DLINEACWDI SSSGVNLQSM DSSHVSLVQL TLRSEGFDTY RCDRNLAMGV NLTSMSKILK CAGNEDIIT LRAEDNADTL ALVFEAPNQE KVSDYEMKLM DLDVEQLGIP EQEYSCVVKM PSGEFARICR DLSHIGDAVV I SCAKDGVK ...String:
MFEARLVQGS ILKKVLEALK DLINEACWDI SSSGVNLQSM DSSHVSLVQL TLRSEGFDTY RCDRNLAMGV NLTSMSKILK CAGNEDIIT LRAEDNADTL ALVFEAPNQE KVSDYEMKLM DLDVEQLGIP EQEYSCVVKM PSGEFARICR DLSHIGDAVV I SCAKDGVK FSASGELGNG NIKLSQTSNV DKEEEAVTIE MNEPVQLTFA LRYLNFFTKA TPLSSTVTLS MSADVPLVVE YK IADMGHL KYYLAPKIED EEGS

UniProtKB: Proliferating cell nuclear antigen

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Macromolecule #4: Fanconi-associated nuclease 1

MacromoleculeName: Fanconi-associated nuclease 1 / type: protein_or_peptide / ID: 4 / 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: 72.856969 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HPYYLRSFLV VLKTVLENED DMLLFDEQEK GIVTKFYQLS ATGQKLYVRL FQRKLSWIKM TKLEYEEIAL DLTPVIEELT NAGFLQTES ELQELSEVLE LLSAPELKSL AKTFHLVNPN GQKQQLVDAF LKLAKQRSVC TWGKNKPGIG AVILKRAKAL A GQSVRICK ...String:
HPYYLRSFLV VLKTVLENED DMLLFDEQEK GIVTKFYQLS ATGQKLYVRL FQRKLSWIKM TKLEYEEIAL DLTPVIEELT NAGFLQTES ELQELSEVLE LLSAPELKSL AKTFHLVNPN GQKQQLVDAF LKLAKQRSVC TWGKNKPGIG AVILKRAKAL A GQSVRICK GPRAVFSRIL LLFSLTDSME DEDAACGGQG QLSTVLLVNL GRMEFPSYTI NRKTHIFQDR DDLIRYAAAT HM LSDISSA MANGNWEEAK ELAQCAKRDW NRLKNHPSLR CHEDLPLFLR CFTVGWIYTR ILSRFVEILQ RLHMYEEAVR ELE SLLSQR IYCPDSRGRW WDRLALNLHQ HLKRLEPTIK CITEGLADPE VRTGHRLSLY QRAVRLRESP SCKKFKHLFQ QLPE MAVQD VKHVTITGRL CPQRGMCKSV FVMEAGEAAD PTTVLCSVEE LALAHYRRSG FDQGIHGEGS TFSTLYGLLL WDIIF MDGI PDVFRNACQA FPLDLCTDSF FTSRRPALEA RLQLIHDAPE ESLRAWVAAT WHEQEGRVAS LVSWDRFTSL QQAQDL VSC LGGPVLSGVC RHLAADFRHC RGGLPDLVVW NSQSRHFKLV EVKGPNDRLS HKQMIWLAEL QKLGAEVEVC HVVAVG

UniProtKB: Fanconi-associated nuclease 1

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 220000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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