[English] 日本語
Yorodumi
- PDB-5k97: Flap endonuclease 1 (FEN1) D233N with cleaved product fragment an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k97
TitleFlap endonuclease 1 (FEN1) D233N with cleaved product fragment 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*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
  • DNA (5'-D(P*TP*T)-3')
  • Flap endonuclease 1
KeywordsHYDROLASE/DNA / METALLOPROTEIN / REPLICATION / DNA DAMAGE / DNA REPAIR / BASE EXCISION REPAIR / PROTEIN-DNA / 5' NUCLEASE / FEN / PRODUCT / HYDROLASE-DNA complex
Function / homology
Function and homology information


positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / nucleic acid metabolic process / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / UV protection / Removal of the Flap Intermediate ...positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / nucleic acid metabolic process / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / UV protection / Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / HDR through MMEJ (alt-NHEJ) / 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 / double-strand break repair / RNA-DNA hybrid ribonuclease activity / manganese ion binding / double-stranded DNA binding / endonuclease activity / DNA replication / chromosome, telomeric region / damaged DNA binding / 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: 2.102 Å
AuthorsTsutakawa, S.E. / Arvai, A.S. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105404 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA92584 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
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 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 1.4Feb 28, 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.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*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
F: DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
G: DNA (5'-D(P*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,26615
Polymers50,9625
Non-polymers1,30410
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-95 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.236, 105.236, 104.548
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

21A-604-

HOH

31A-930-

HOH

-
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: D233N
Source method: isolated from a genetically manipulated source
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 , 4 types, 4 molecules DEFG

#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 / Details: DNA oligonucleotide synthesis / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')


Mass: 3438.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide synthesis / 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 / Details: DNA oligonucleotide synthesis / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(P*TP*T)-3')


Mass: 1479.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide synthesis / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 633 molecules

#6: Chemical
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Sm
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 24% MPEG 2K, 20% KCl, 5% ethylene glycol, 100 mM HEPES pH 7.5
PH range: ?76.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 39124 / % possible obs: 99.5 % / Redundancy: 13.8 % / Biso Wilson estimate: 42.47 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.025 / Rrim(I) all: 0.095 / Χ2: 6.084 / Net I/av σ(I): 73.898 / Net I/σ(I): 18.4 / Num. measured all: 539312
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.1810.40.651197.5
2.18-2.2613.20.4681100
2.26-2.3714.20.3271100
2.37-2.4914.30.2381100
2.49-2.6514.40.1761100
2.65-2.8514.40.1351100
2.85-3.1414.40.1061100
3.14-3.5914.50.091100
3.59-4.5214.30.0811100
4.52-5013.60.071197.6

-
Phasing

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

-
Processing

Software
NameVersionClassification
PHENIX(dev_2383: ???)refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.102→34.849 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 3830 5.12 %
Rwork0.1824 --
obs0.1843 74847 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.102→34.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 772 13 623 4107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043718
X-RAY DIFFRACTIONf_angle_d0.5315134
X-RAY DIFFRACTIONf_dihedral_angle_d15.9522153
X-RAY DIFFRACTIONf_chiral_restr0.04565
X-RAY DIFFRACTIONf_plane_restr0.003540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.102-2.12860.36911250.3352350X-RAY DIFFRACTION89
2.1286-2.15660.33741390.31792595X-RAY DIFFRACTION98
2.1566-2.18620.28111420.28062701X-RAY DIFFRACTION100
2.1862-2.21740.29711500.25912598X-RAY DIFFRACTION100
2.2174-2.25050.2661460.24162663X-RAY DIFFRACTION100
2.2505-2.28560.251480.24212649X-RAY DIFFRACTION100
2.2856-2.32310.25131420.22222607X-RAY DIFFRACTION100
2.3231-2.36320.23681360.21292656X-RAY DIFFRACTION100
2.3632-2.40610.25831480.21412625X-RAY DIFFRACTION100
2.4061-2.45240.25631420.20962684X-RAY DIFFRACTION100
2.4524-2.50240.20191360.20612704X-RAY DIFFRACTION100
2.5024-2.55680.22091400.20892626X-RAY DIFFRACTION100
2.5568-2.61630.28991440.20812613X-RAY DIFFRACTION100
2.6163-2.68170.2821370.21152652X-RAY DIFFRACTION100
2.6817-2.75420.2181400.20372682X-RAY DIFFRACTION100
2.7542-2.83520.27371400.20482663X-RAY DIFFRACTION100
2.8352-2.92670.29241460.21272608X-RAY DIFFRACTION100
2.9267-3.03120.20261420.20192659X-RAY DIFFRACTION100
3.0312-3.15250.27461420.21212658X-RAY DIFFRACTION100
3.1525-3.29590.24421450.18752661X-RAY DIFFRACTION100
3.2959-3.46950.18811360.17252617X-RAY DIFFRACTION100
3.4695-3.68660.21661520.16022625X-RAY DIFFRACTION100
3.6866-3.97090.1711440.15152671X-RAY DIFFRACTION100
3.9709-4.36980.17091440.13712674X-RAY DIFFRACTION100
4.3698-5.00060.15311460.13122621X-RAY DIFFRACTION100
5.0006-6.29410.21641400.16032643X-RAY DIFFRACTION100
6.2941-34.85410.22241380.19242512X-RAY DIFFRACTION94

+
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://pdbjlvh1.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