[English] 日本語
Yorodumi
- PDB-6nju: Mouse endonuclease G mutant H97A bound to A-DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nju
TitleMouse endonuclease G mutant H97A bound to A-DNA
Components
  • DNA (5'-D(CCGGCGCCGG)-3')
  • Endonuclease G, mitochondrialENDOG
KeywordsRECOMBINATION / Complex / Endonuclease
Function / homology
Function and homology information


mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of mitochondrial DNA replication / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / DNA nuclease activity / positive regulation of apoptotic DNA fragmentation / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / negative regulation of TOR signaling / DNA catabolic process ...mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of mitochondrial DNA replication / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / DNA nuclease activity / positive regulation of apoptotic DNA fragmentation / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / negative regulation of TOR signaling / DNA catabolic process / response to tumor necrosis factor / positive regulation of autophagy / RNA endonuclease activity / DNA endonuclease activity / perikaryon / in utero embryonic development / mitochondrial inner membrane / nucleic acid binding / positive regulation of apoptotic process / response to antibiotic / DNA damage response / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / mitochondrion / nucleus
Similarity search - Function
DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily
Similarity search - Domain/homology
DNA / Endonuclease G, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVander Zanden, C.M. / Ho, E.N. / Czarny, R.S. / Robertson, A.B. / Ho, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1515521 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function.
Authors: Vander Zanden, C.M. / Czarny, R.S. / Ho, E.N. / Robertson, A.B. / Ho, P.S.
History
DepositionJan 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Mar 11, 2020Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Oct 11, 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 / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endonuclease G, mitochondrial
B: Endonuclease G, mitochondrial
C: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial
E: DNA (5'-D(CCGGCGCCGG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,97414
Polymers114,6135
Non-polymers3619
Water4,360242
1
C: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial
E: DNA (5'-D(CCGGCGCCGG)-3')
hetero molecules

C: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial
E: DNA (5'-D(CCGGCGCCGG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,21418
Polymers117,6606
Non-polymers55412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
2
A: Endonuclease G, mitochondrial
B: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8675
Polymers55,7832
Non-polymers843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-56 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.983, 107.983, 357.419
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

-
Protein / DNA chain , 2 types, 5 molecules ABCDE

#1: Protein
Endonuclease G, mitochondrial / ENDOG / Endo G


Mass: 27891.410 Da / Num. of mol.: 4 / Fragment: residues 43-294 / Mutation: H97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Endog / Plasmid: pMal-c2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: O08600, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
#2: DNA chain DNA (5'-D(CCGGCGCCGG)-3')


Mass: 3046.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

-
Non-polymers , 4 types, 251 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.64 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.5, 22% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 22, 2017
RadiationMonochromator: ROSENBAUM-ROCK SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.35→59.57 Å / Num. obs: 52587 / % possible obs: 99.9 % / Redundancy: 20.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.814 / Rpim(I) all: 0.256 / Net I/σ(I): 5.1
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 19.5 % / Rmerge(I) obs: 6.791 / Num. unique obs: 4441 / CC1/2: 0.343 / Rpim(I) all: 2.231 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
XDSdata reduction
PHASERv2.7.16phasing
Cootv0.8.9.1model building
Aimlessv0.7.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GKP

5gkp


Resolution: 2.35→53.992 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.85
RfactorNum. reflection% reflection
Rfree0.2915 2533 4.83 %
Rwork0.2223 --
obs0.2256 52389 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.43 Å2 / Biso mean: 35.7824 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: final / Resolution: 2.35→53.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7213 202 16 243 7674
Biso mean--38.87 32.03 -
Num. residues----914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.39520.42311360.36462697283399
2.3952-2.44410.37251520.343226732825100
2.4441-2.49730.37331570.314126802837100
2.4973-2.55540.36591360.296727272863100
2.5554-2.61930.3491360.288927212857100
2.6193-2.69010.36531280.285927402868100
2.6901-2.76930.35081340.268427382872100
2.7693-2.85860.33571330.250527322865100
2.8586-2.96080.30741460.248527132859100
2.9608-3.07930.35231330.245827642897100
3.0793-3.21950.27461400.222427422882100
3.2195-3.38920.27711440.211727732917100
3.3892-3.60150.28251300.194727912921100
3.6015-3.87950.28241300.188327782908100
3.8795-4.26970.26541270.175328172944100
4.2697-4.88720.2271610.164328152976100
4.8872-6.1560.24871570.190528593016100
6.156-54.00570.23711530.205530963249100

+
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