[English] 日本語
Yorodumi
- PDB-6lwm: Crystal structure of human NEIL1(K242) bound to duplex DNA contai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lwm
TitleCrystal structure of human NEIL1(K242) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
  • DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
  • Endonuclease 8-like 1
KeywordsDNA BINDING PROTEIN/DNA / Base lesion / Oxidative DNA damage / DNA repair / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of nuclease 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 / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity ...negative regulation of nuclease 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 / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / chromosome / response to oxidative stress / damaged DNA binding / centrosome / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Endonuclease VIII-like 1, DNA binding / Endonuclease VIII-like 1, DNA bind / 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 / Ribosomal protein S13-like, H2TH
Similarity search - Domain/homology
DNA / DNA (> 10) / Endonuclease 8-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsLiu, M.H. / Zhang, J. / Zhu, C.X. / Zhang, X.X. / Gao, Y.Q. / Yi, C.Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91953201 China
National Natural Science Foundation of China (NSFC)21825701 China
CitationJournal: Nat Commun / Year: 2021
Title: DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes.
Authors: Liu, M. / Zhang, J. / Zhu, C. / Zhang, X. / Xiao, W. / Yan, Y. / Liu, L. / Zeng, H. / Gao, Y.Q. / Yi, C.
History
DepositionFeb 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: 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.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endonuclease 8-like 1
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
C: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
D: Endonuclease 8-like 1
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
F: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
G: Endonuclease 8-like 1
H: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
I: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,77110
Polymers123,6799
Non-polymers921
Water3,621201
1
A: Endonuclease 8-like 1
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
C: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3184
Polymers41,2263
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-13 kcal/mol
Surface area15930 Å2
MethodPISA
2
D: Endonuclease 8-like 1
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
F: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)41,2263
Polymers41,2263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-15 kcal/mol
Surface area16070 Å2
MethodPISA
3
G: Endonuclease 8-like 1
H: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')
I: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)41,2263
Polymers41,2263
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-11 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.693, 109.246, 170.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 33301.219 Da / Num. of mol.: 3
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 (5'-D(*CP*GP*TP*CP*CP*AP*(FDU)P*GP*TP*CP*TP*AP*C)-3')


Mass: 3908.528 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Oligo DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')


Mass: 4016.623 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: TAGACCTGGACGG / Source: (synth.) Escherichia coli (E. coli)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.76 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 39614 / % possible obs: 99.3 % / Redundancy: 5 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.041 / Rrim(I) all: 0.092 / Χ2: 1.44 / Net I/σ(I): 11.4 / Num. measured all: 198604
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.67-2.725.20.99219530.6930.4781.1031.3100
2.72-2.775.20.8719550.7410.4190.9671.31399.9
2.77-2.825.20.69119760.8210.3330.7681.344100
2.82-2.885.20.56219570.8710.2710.6251.374100
2.88-2.945.20.4519780.920.2160.51.35799.9
2.94-3.015.20.38219500.930.1840.4251.362100
3.01-3.085.20.29719620.960.1430.331.412100
3.08-3.175.20.21319720.9790.1020.2361.458100
3.17-3.265.20.16519740.9850.0790.1831.5599.9
3.26-3.365.20.13519850.9880.0650.151.58799.9
3.36-3.485.20.10919740.9920.0530.1211.5699.7
3.48-3.625.20.0919570.9950.0430.11.57499.5
3.62-3.795.10.07719770.9950.0370.0851.51399.6
3.79-3.9950.07419860.9950.0360.0821.4699.8
3.99-4.244.90.06919930.9950.0350.0781.41599.6
4.24-4.564.70.06319970.9950.0330.0721.4799.3
4.56-5.024.50.0619900.9950.0320.0691.49299
5.02-5.754.60.06119980.9950.0320.0691.38998.6
5.75-7.244.70.04620480.9980.0230.0511.37399.3
7.24-504.60.03720320.9970.0190.0421.50593.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ITY

5ity


Resolution: 2.67→39.45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 23.606 / SU ML: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.553 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 2010 5.1 %RANDOM
Rwork0.2048 ---
obs0.2075 37542 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.49 Å2 / Biso mean: 81.369 Å2 / Biso min: 35.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å2-0 Å2
2---1.61 Å20 Å2
3---2.98 Å2
Refinement stepCycle: final / Resolution: 2.67→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 1575 6 201 7479
Biso mean--100.8 67.33 -
Num. residues----825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0127603
X-RAY DIFFRACTIONr_bond_other_d0.0030.0186297
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.54210577
X-RAY DIFFRACTIONr_angle_other_deg1.3511.78414491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6835733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33419.942344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81115896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0031565
X-RAY DIFFRACTIONr_chiral_restr0.0790.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027697
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021881
LS refinement shellResolution: 2.672→2.741 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 137 -
Rwork0.305 2710 -
all-2847 -
obs--97.3 %
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)
13.1662.38350.23216.39291.87451.8235-0.19780.2030.0172-0.32470.2951-0.450.05010.0999-0.09720.0379-0.0060.05430.03450.04470.2445-8.711-8.76835.789
211.3977-4.012-3.03283.77250.75422.55480.35521.1582-0.2041-0.6011-0.3160.1119-0.08330.4163-0.03920.4401-0.01910.08660.4415-0.09170.5641-1.206-15.75519.851
37.1188-1.7849-1.010510.12373.27713.14540.0417-0.0664-0.2601-0.50370.2239-0.02540.3618-0.2563-0.26560.40070.00410.24690.46230.03970.50923.812-18.31320.215
45.6026-1.8462-0.05824.3252-0.31733.8681-0.2434-0.2744-0.38240.26170.11530.15440.1865-0.05330.1280.0720.03240.0440.0355-0.00610.157-29.4898.10451.444
58.77471.1187-4.4333.67870.43236.248-0.22-0.890.2720.64780.06970.3474-0.1-0.17140.15030.38570.1321-0.04390.44240.03190.275-35.84217.35866.252
68.16950.9733.19614.3373-0.572511.5657-0.2737-1.057-0.46620.99390.2758-0.0291-0.0308-0.268-0.00210.42050.18680.26090.44410.07910.4012-40.56115.50568.516
75.2592-0.0645-2.63242.0983-0.00514.17930.3116-0.0062-0.1422-0.4219-0.20390.0652-0.2804-0.1809-0.10770.9620.1309-0.07220.7719-0.16430.3232-43.2429.0474.455
89.2932-0.99733.16031.67710.95635.1357-0.05160.1012-1.0516-0.41230.1498-0.1307-0.220.0634-0.09820.8757-0.00810.03360.89050.07070.6224-36.896-6.255-0.789
98.89680.19091.5444.1815-2.0942.3341-0.0518-0.4188-0.57140.24630.17610.17060.3763-0.0337-0.12440.87110.08870.04180.9337-0.10090.6335-32.395-7.6961.571
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 290
2X-RAY DIFFRACTION2B1 - 13
3X-RAY DIFFRACTION3C1 - 13
4X-RAY DIFFRACTION4D2 - 290
5X-RAY DIFFRACTION5E1 - 13
6X-RAY DIFFRACTION6F1 - 13
7X-RAY DIFFRACTION7G2 - 289
8X-RAY DIFFRACTION8H1 - 13
9X-RAY DIFFRACTION9I1 - 13

+
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