[English] 日本語
Yorodumi
- EMDB-51680: Cryo_EM structure of human FAN1 R507H mutant in complex with 5' f... -

+
Open data


ID or keywords:

Loading...

-
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 / purine-specific mismatch base pair DNA N-glycosylase activity / 5'-flap endonuclease activity / MutLalpha complex binding / nuclear lamina ...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 / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / 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 / DNA polymerase processivity factor activity / intercellular bridge / 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 / response to cadmium ion / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / DNA polymerase binding / base-excision repair, gap-filling / epithelial cell differentiation / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / male germ cell nucleus / Translesion synthesis by REV1 / Translesion synthesis by POLK / liver regeneration / 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 / 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 / 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
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
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 TF / Boudet J / Prasad BC
History
DepositionOct 1, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51680.png

Downloads & links

-
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 °

-
Supplemental data

-
Half map: #1

Fileemd_51680_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51680_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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)

-
Supramolecule #3: DNA

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

-
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

-
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

-
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)

-
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)

-
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)

-
Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

-
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

+
Image processing

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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more