[English] 日本語
Yorodumi
- PDB-5itr: Crystal Structure of Human NEIL1(P2G) bound to duplex DNA contain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5itr
TitleCrystal Structure of Human NEIL1(P2G) bound to duplex DNA containing THF
Components
  • (DNA (26-MER)) x 2
  • Endonuclease 8-like 1
KeywordsDNA BINDING PROTEIN/DNA / DNA glycosylase NEIL1 Fpg Nei base excision repair / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity ...: / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / base-excision repair / chromosome / response to oxidative stress / damaged DNA binding / centrosome / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Endonuclease VIII-like 1, DNA binding / Endonuclease VIII-like 1, DNA bind / MutM-like, N-terminal / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain ...Endonuclease VIII-like 1, DNA binding / Endonuclease VIII-like 1, DNA bind / MutM-like, N-terminal / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Endonuclease 8-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsZhu, C. / Lu, L. / Zhang, J. / Yue, Z. / Song, J. / Zong, S. / Liu, M. / Stovicek, O. / Gao, Y. / Yi, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair
Authors: Zhu, C. / Lu, L. / Zhang, J. / Yue, Z. / Song, J. / Zong, S. / Liu, M. / Stovicek, O. / Gao, Y.Q. / Yi, C.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endonuclease 8-like 1
B: Endonuclease 8-like 1
C: Endonuclease 8-like 1
D: DNA (26-MER)
E: DNA (26-MER)
F: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)158,6396
Polymers158,6396
Non-polymers00
Water2,252125
1
A: Endonuclease 8-like 1
D: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)52,8742
Polymers52,8742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-6 kcal/mol
Surface area15910 Å2
MethodPISA
2
B: Endonuclease 8-like 1
E: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)52,8742
Polymers52,8742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-7 kcal/mol
Surface area16100 Å2
MethodPISA
3
C: Endonuclease 8-like 1
F: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)52,8902
Polymers52,8902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-7 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.306, 109.036, 169.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endonuclease 8-like 1 / DNA glycosylase/AP lyase Neil1 / DNA-(apurinic or apyrimidinic site) lyase Neil1 / Endonuclease ...DNA glycosylase/AP lyase Neil1 / DNA-(apurinic or apyrimidinic site) lyase Neil1 / Endonuclease VIII-like 1 / FPG1 / Nei homolog 1 / NEH1 / Nei-like protein 1


Mass: 44925.371 Da / Num. of mol.: 3 / Mutation: K242R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEIL1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96FI4, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain DNA (26-MER)


Mass: 7949.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: DNA chain DNA (26-MER)


Mass: 7965.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5
Details: 0.1M cacodylic acid (pH 7.0), 0.1M NaCl, 0.05 M MgCl2, 24%(w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.46→91.75 Å / Num. obs: 47431 / % possible obs: 99.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.077 / Rsym value: 0.06 / Net I/σ(I): 22.58
Reflection shellResolution: 2.46→2.52 Å / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TDH

1tdh


Resolution: 2.46→91.75 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2488 5 %RANDOM
Rwork0.211 ---
obs0.213 47431 99.4 %-
Refinement stepCycle: LAST / Resolution: 2.46→91.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 1549 0 125 7910
LS refinement shellResolution: 2.46→2.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 188 -
Rwork0.323 3366 -
obs--96.08 %

+
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