[English] 日本語
Yorodumi
- PDB-5um9: Flap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and Sm3+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5um9
TitleFlap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and Sm3+
Components
  • DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
  • DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')
  • DNA (5'-D(P*TP*CP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
  • Flap endonuclease 1
KeywordsHydrolase/DNA / dna repair / endonuclease / 5' nuclease / DNA binding / Hydrolase-DNA complex
Function / homology
Function and homology information


flap endonuclease activity / positive regulation of sister chromatid cohesion / telomere maintenance via semi-conservative replication / nucleic acid metabolic process / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / UV protection / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) ...flap endonuclease activity / positive regulation of sister chromatid cohesion / telomere maintenance via semi-conservative replication / nucleic acid metabolic process / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / UV protection / 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 / DNA replication / damaged DNA binding / chromosome, telomeric region / Hydrolases; Acting on ester bonds / DNA repair / nucleolus / magnesium ion binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / membrane / nucleus
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 / 5'-nuclease / 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 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / SAMARIUM (III) ION / DNA / DNA (> 10) / Flap endonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.805 Å
AuthorsTsutakawa, S.E. / Arvai, A.S. / Tainer, J.A.
Funding support United States, Saudi Arabia, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)PO1CA92584 United States
KAUST Saudi Arabia
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105404 United States
CitationJournal: Nat Commun / Year: 2017
Title: Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability.
Authors: Tsutakawa, S.E. / Thompson, M.J. / Arvai, A.S. / Neil, A.J. / Shaw, S.J. / Algasaier, S.I. / Kim, J.C. / Finger, L.D. / Jardine, E. / Gotham, V.J.B. / Sarker, A.H. / Her, M.Z. / Rashid, F. / ...Authors: Tsutakawa, S.E. / Thompson, M.J. / Arvai, A.S. / Neil, A.J. / Shaw, S.J. / Algasaier, S.I. / Kim, J.C. / Finger, L.D. / Jardine, E. / Gotham, V.J.B. / Sarker, A.H. / Her, M.Z. / Rashid, F. / Hamdan, S.M. / Mirkin, S.M. / Grasby, J.A. / Tainer, J.A.
History
DepositionJan 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flap endonuclease 1
D: DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')
E: DNA (5'-D(P*TP*CP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
F: DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,10210
Polymers51,3124
Non-polymers7916
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.846, 105.846, 100.709
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 38510.203 Da / Num. of mol.: 1 / Mutation: D86N
Source method: isolated from a genetically manipulated source
Details: Mutation D86N / Source: (gene. exp.) Homo sapiens (human) / Gene: FEN1, RAD2 / Production host: Escherichia coli (E. coli)
References: UniProt: P39748, Hydrolases; Acting on ester bonds

-
DNA chain , 3 types, 3 molecules DEF

#2: DNA chain DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')


Mass: 5476.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*CP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')


Mass: 5266.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')


Mass: 2058.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 41 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Sm
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 6% MPEG 2K, 10% KCl, 50 mM HEPES pH 7.5, 2.5% Ethylene glycol, 1.06 mM SmSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.805→19.672 Å / Num. obs: 30759 / % possible obs: 99 % / Redundancy: 16.3 % / Biso Wilson estimate: 98.43 Å2 / Net I/σ(I): 31.28

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALAdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.805→19.672 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.87
RfactorNum. reflection% reflection
Rfree0.2659 1548 5.03 %
Rwork0.2078 --
obs0.2107 30759 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 255.62 Å2 / Biso mean: 122.3541 Å2 / Biso min: 52.31 Å2
Refinement stepCycle: final / Resolution: 2.805→19.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 790 6 35 3529
Biso mean--134.73 110.5 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083643
X-RAY DIFFRACTIONf_angle_d0.5685046
X-RAY DIFFRACTIONf_chiral_restr0.04559
X-RAY DIFFRACTIONf_plane_restr0.003522
X-RAY DIFFRACTIONf_dihedral_angle_d19.3731447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8053-2.89560.49271380.41672631276999
2.8956-2.99870.33281480.341426472795100
2.9987-3.11830.34371420.308726742816100
3.1183-3.25960.34231360.294526652801100
3.2596-3.43060.36641400.270126572797100
3.4306-3.64430.26411370.245626602797100
3.6443-3.92360.29011460.220226872833100
3.9236-4.31470.23381420.206326312773100
4.3147-4.93050.22451450.170526482793100
4.9305-6.17980.26871340.200826822816100
6.1798-19.6730.24451400.17062629276999

+
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