[English] 日本語
Yorodumi
- PDB-9rci: Crystal Structure of Flap Endonuclease FEN1 with Compound 28 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rci
TitleCrystal Structure of Flap Endonuclease FEN1 with Compound 28
ComponentsFlap endonuclease 1
KeywordsHYDROLASE / Endonuclease
Function / homology
Function and homology information


flap endonuclease activity / telomere maintenance via semi-conservative replication / positive regulation of sister chromatid cohesion / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / UV protection / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand ...flap endonuclease activity / telomere maintenance via semi-conservative replication / positive regulation of sister chromatid cohesion / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / UV protection / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand / 5'-3' exonuclease activity / exonuclease activity / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / double-strand break repair via homologous recombination / memory / RNA-DNA hybrid ribonuclease activity / double-strand break repair / manganese ion binding / double-stranded DNA binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA replication / DNA repair / nucleolus / magnesium ion binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily
Similarity search - Domain/homology
: / Flap endonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.662 Å
AuthorsToste Rego, A. / Pica, A. / Cornaciu, I. / Burgdorf, L. / Mann, S.E.
Funding support United Kingdom, Germany, 2items
OrganizationGrant numberCountry
Other private United Kingdom
Other private Germany
CitationJournal: J.Med.Chem. / Year: 2025
Title: Fragment-Based Discovery and Structure-Led Optimization of MSC778, the First Potent, Selective, and Orally Bioavailable FEN1 Inhibitor.
Authors: Mann, S.E. / Lefranc, J. / Alkhatib, O. / Boivin, R. / Bomke, J. / Byrne, R.T. / Cassona, C.P. / Chen, X. / Cornaciu, I. / Costales, P. / Davis, O.A. / DeSelm, L. / Elinati, E. / Follows, B. ...Authors: Mann, S.E. / Lefranc, J. / Alkhatib, O. / Boivin, R. / Bomke, J. / Byrne, R.T. / Cassona, C.P. / Chen, X. / Cornaciu, I. / Costales, P. / Davis, O.A. / DeSelm, L. / Elinati, E. / Follows, B. / Galbiati, A. / Goldner, C. / Hayre, J.K. / Jorand-Lebrun, C. / Lademann, C.A. / Leuthner, B. / Majithiya, J.B. / Malta, C.F. / Mason, B. / McWhirter, C.L. / Neff, B. / Nissink, J.W.M. / Pehl, U. / Petersson, C. / Pica, A. / Pinto, M.F. / Rajendra, E. / Rakers, C. / Toste Rego, A. / Robinson, H.M.R. / Sala-Hojman, A. / Schaedler, T.A. / Schurmann, P.J.L. / Silva, D.O. / Smith, G.C.M. / Sorrell, F. / Webster, G.R. / Zenke, F.T. / Heald, R.A. / Burgdorf, L.T.
History
DepositionMay 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flap endonuclease 1
B: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,34910
Polymers77,2852
Non-polymers1,0648
Water3,297183
1
A: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1755
Polymers38,6421
Non-polymers5324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1755
Polymers38,6421
Non-polymers5324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.869, 39.297, 100.916
Angle α, β, γ (deg.)98.30, 90.32, 90.09
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Flap endonuclease 1 / FEN-1 / DNase IV / Flap structure-specific endonuclease 1 / Maturation factor 1 / MF1 / hFEN-1


Mass: 38642.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FEN1, RAD2 / Production host: Escherichia coli (E. coli) / Strain (production host): E.coli RIL
References: UniProt: P39748, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1JD4 / (3~{S})-13-[(1~{S})-1-(2-methylquinolin-7-yl)ethoxy]-11-oxidanyl-5-oxa-1,8-diazatricyclo[8.4.0.0^{3,8}]tetradeca-10,13-diene-9,12-dione


Mass: 421.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23N3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 21 % PEG MME 5000, 0.1 M MES pH 6.5, 10 mM ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.662→99.857 Å / Num. obs: 44821 / % possible obs: 87.6 % / Redundancy: 1.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.103 / Rrim(I) all: 0.198 / Net I/σ(I): 4.3
Reflection shellResolution: 1.662→1.811 Å / Rmerge(I) obs: 0.859 / Num. unique obs: 2241 / CC1/2: 0.525 / Rpim(I) all: 0.518

-
Processing

Software
NameVersionClassification
BUSTER2.11.8 (10-JUL-2024)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.662→33.08 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.851 / SU R Cruickshank DPI: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.168
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2833 2159 4.82 %RANDOM
Rwork0.2437 ---
obs0.2456 44812 69.8 %-
Displacement parametersBiso mean: 20.93 Å2
Baniso -1Baniso -2Baniso -3
1--5.2061 Å20.9315 Å2-0.0919 Å2
2---2.0918 Å2-3.1848 Å2
3---7.2979 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.662→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 74 183 4459
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014458HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.026073HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1571SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes771HARMONIC5
X-RAY DIFFRACTIONt_it4336HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion17.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion568SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3801SEMIHARMONIC4
LS refinement shellResolution: 1.662→1.76 Å
RfactorNum. reflection% reflection
Rfree0.2418 -3.9 %
Rwork-862 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4047-0.1221-0.27650.43910.52280.77430.03470.0293-0.01170.01690.0171-0.0133-0.05280.0441-0.0518-0.11580.0169-0.0095-0.0657-0.05040.1196-4.98722.9127-27.8333
20.37730.1627-0.32140.3355-0.38270.72710.0321-0.03340.0034-0.02730.01160.0216-0.0386-0.0615-0.0438-0.10240.0137-0.0015-0.0503-0.05360.11311.595317.741-80.0624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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