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- PDB-9eoa: Cryo_EM structure of human FAN1 in complex with 5' flap DNA subst... -

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Basic information

Entry
Database: PDB / ID: 9eoa
TitleCryo_EM structure of human FAN1 in complex with 5' flap DNA substrate and PCNA
Components
  • DNA (continuous)
  • DNA (post-nick)
  • DNA (pre-nick)
  • Fanconi-associated nuclease 1
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / FAN1 / PCNA
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 / purine-specific mismatch base pair DNA N-glycosylase activity / 5'-flap endonuclease activity / MutLalpha complex binding / 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 / purine-specific mismatch base pair DNA N-glycosylase activity / 5'-flap endonuclease activity / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina / Telomere C-strand (Lagging Strand) Synthesis / Polymerase switching / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / 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) / Removal of the Flap Intermediate from the C-strand / Transcription of E2F targets under negative control by DREAM complex / ubiquitin-modified protein reader activity / replisome / 5'-3' exonuclease activity / phosphodiesterase I activity / response to L-glutamate / histone acetyltransferase binding / intercellular bridge / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / replication fork processing / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / translesion synthesis / interstrand cross-link repair / DNA polymerase binding / response to cadmium ion / cyclin-dependent protein kinase holoenzyme complex / estrous cycle / base-excision repair, gap-filling / 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 / male germ cell nucleus / replication fork / positive regulation of DNA replication / nuclear estrogen receptor binding / nucleotide-excision repair / liver regeneration / 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 / HDR through Homologous Recombination (HRR) / receptor tyrosine kinase binding / 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 / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / damaged DNA binding / chromosome, telomeric region / nuclear body / 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 / 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
DNA / DNA (> 10) / Proliferating cell nuclear antigen / Fanconi-associated nuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsJeyasankar, G. / Salerno-Kochan, A. / Thomsen, M.
Funding support United States, 1items
OrganizationGrant numberCountry
CHDI Foundation United States
CitationJournal: 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, T.F. / Boudet, J. / Prasad, B.C.
History
DepositionMar 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fanconi-associated nuclease 1
B: DNA (continuous)
C: DNA (pre-nick)
D: DNA (post-nick)
F: Proliferating cell nuclear antigen
G: Proliferating cell nuclear antigen
H: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)184,7927
Polymers184,7927
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Fanconi-associated nuclease 1 / FANCD2/FANCI-associated nuclease 1 / hFAN1 / Myotubularin-related protein 15


Mass: 72629.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAN1, KIAA1018, MTMR15 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y2M0, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters, phosphodiesterase I
#2: DNA chain DNA (continuous)


Mass: 12154.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (pre-nick)


Mass: 8618.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (post-nick)


Mass: 6554.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Protein Proliferating cell nuclear antigen / PCNA / Cyclin


Mass: 28278.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12004
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Ternary complex of FAN1-PCNA-DNACOMPLEXall0MULTIPLE SOURCES
2FAN1-PCNACOMPLEX#1-#21RECOMBINANT
3DNACOMPLEX#3-#51RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 700432 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412128
ELECTRON MICROSCOPYf_angle_d0.65716658
ELECTRON MICROSCOPYf_dihedral_angle_d18.5772089
ELECTRON MICROSCOPYf_chiral_restr0.0431922
ELECTRON MICROSCOPYf_plane_restr0.0041905

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