[English] 日本語
Yorodumi
- PDB-7r6t: Human EXOG complexed with dRP-containing DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r6t
TitleHuman EXOG complexed with dRP-containing DNA
Components
  • DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
  • DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
  • Nuclease EXOG, mitochondrial
KeywordsDNA BINDING PROTEIN/DNA / Mitochondrial BER / endo/exonuclease / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / mitochondrial inner membrane / nucleic acid binding / protein-containing complex / mitochondrion ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / mitochondrial inner membrane / nucleic acid binding / protein-containing complex / mitochondrion / metal ion binding / nucleus
Similarity search - Function
EXOG, C-terminal / Endo/exonuclease (EXOG) C-terminal domain / 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 / DNA (> 10) / Nuclease EXOG, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSzymanski, M.R. / Yin, Y.W.
CitationJournal: To Be Published
Title: Human EXOG possesses strong AP hydrolysis activity
Authors: Szymanski, M.R. / Yin, Y.W.
History
DepositionJun 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Nuclease EXOG, mitochondrial
F: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
A: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
C: Nuclease EXOG, mitochondrial
E: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
B: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
L: Nuclease EXOG, mitochondrial
M: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
K: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,21814
Polymers125,0989
Non-polymers1205
Water19811
1
D: Nuclease EXOG, mitochondrial
F: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
A: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7485
Polymers41,6993
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nuclease EXOG, mitochondrial
E: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
B: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7475
Polymers41,6993
Non-polymers472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
L: Nuclease EXOG, mitochondrial
M: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
K: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7244
Polymers41,6993
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.252, 100.056, 174.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 3 molecules DCL

#1: Protein Nuclease EXOG, mitochondrial / Endonuclease G-like 1 / Endo G-like 1


Mass: 35444.203 Da / Num. of mol.: 3 / Mutation: H140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOG, ENDOGL1, ENDOGL2, ENGL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y2C4, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters

-
DNA chain , 2 types, 6 molecules FEMABK

#2: DNA chain DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')


Mass: 2911.894 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The mismatch is due to a deoxyribose site. / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')


Mass: 3343.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 16 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% PEG 4K, 0.2 M Ammonium Acetate, 0.1 M Na Citrate tribasic dihydrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2021
RadiationMonochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 26817 / % possible obs: 99 % / Redundancy: 6.4 % / CC1/2: 0.75 / Net I/σ(I): 2.7
Reflection shellResolution: 2.9→3.5 Å / Redundancy: 6.3 % / Num. unique obs: 2612 / CC1/2: 0.5

-
Processing

Software
NameVersionClassification
PHENIX1.17refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T5C

5t5c


Resolution: 2.9→37.97 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.286 --
Rwork0.229 --
obs-26817 99 %
Displacement parametersBiso mean: 92.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6781 1012 5 11 7809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00298074
X-RAY DIFFRACTIONf_angle_d0.535311155
X-RAY DIFFRACTIONf_chiral_restr0.04251226
X-RAY DIFFRACTIONf_plane_restr0.00381284
X-RAY DIFFRACTIONf_dihedral_angle_d14.23374645

+
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