[English] 日本語
Yorodumi
- PDB-5t3v: A Novel domain in human EXOG converts apoptotic endonuclease to D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t3v
TitleA Novel domain in human EXOG converts apoptotic endonuclease to DNA-repair enzyme
ComponentsNuclease EXOG, mitochondrial
KeywordsHYDROLASE / mitochondria / exonuclease / DNA-repair / 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 / single-stranded DNA endodeoxyribonuclease activity / apoptotic DNA fragmentation / Strand-asynchronous mitochondrial DNA replication / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / protein-containing complex ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / single-stranded DNA endodeoxyribonuclease activity / apoptotic DNA fragmentation / Strand-asynchronous mitochondrial DNA replication / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / 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; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease ...EXOG, C-terminal / Endo/exonuclease (EXOG) C-terminal domain / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Nuclease EXOG, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSzymanski, M.R. / Yin, W.Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 083703 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 110591 United States
CitationJournal: Nat Commun / Year: 2017
Title: A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease.
Authors: Szymanski, M.R. / Yu, W. / Gmyrek, A.M. / White, M.A. / Molineux, I.J. / Lee, J.C. / Yin, Y.W.
History
DepositionAug 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclease EXOG, mitochondrial
B: Nuclease EXOG, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9866
Polymers72,6842
Non-polymers3024
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-77 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.340, 83.436, 74.771
Angle α, β, γ (deg.)90.000, 113.420, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 36342.219 Da / Num. of mol.: 2 / Fragment: UNP residues 59-368
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
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 2M (NH4)2SO4, 0.1M MgCl2, 0.1M Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.89 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 2.6→49.708 Å / Num. obs: 24211 / % possible obs: 95.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ISM

3ism


Resolution: 2.6→49.708 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.96
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 1993 8.23 %8.21%
Rwork0.1758 ---
obs0.1798 24211 94.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.79 Å2 / Biso mean: 69.9715 Å2 / Biso min: 24.48 Å2
Refinement stepCycle: final / Resolution: 2.6→49.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 12 81 4910
Biso mean--127.37 48.3 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034941
X-RAY DIFFRACTIONf_angle_d0.4836685
X-RAY DIFFRACTIONf_chiral_restr0.043717
X-RAY DIFFRACTIONf_plane_restr0.003869
X-RAY DIFFRACTIONf_dihedral_angle_d13.1322993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5999-2.66490.31361300.25071461159188
2.6649-2.7370.34261390.24171502164191
2.737-2.81750.33581390.25581550168992
2.8175-2.90840.29931310.24851545167693
2.9084-3.01240.27721460.22211560170694
3.0124-3.1330.25991380.21421575171395
3.133-3.27550.2691450.20661598174395
3.2755-3.44820.29621430.20431593173696
3.4482-3.66420.22281350.17441616175196
3.6642-3.9470.19761520.15051602175497
3.947-4.3440.18211440.13621637178197
4.344-4.9720.15391460.12151634178097
4.972-6.26230.1911480.15111662181098
6.2623-49.7170.2241570.18731683184098
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)
15.9692-0.4322.04632.76240.16092.9859-0.2130.02450.249-0.2660.1605-0.01310.0893-0.19710.00080.358-0.00490.0360.26080.00360.3431-12.939128.2775-10.8295
23.9765-0.3871.52138.6637-0.29666.57060.1570.8613-0.1717-0.7666-0.2171-0.05890.09940.09610.0020.47960.0070.05720.5402-0.03160.2626-11.926318.0906-21.8648
32.2167-0.97040.91962.6043-0.68441.9643-0.02430.0142-0.0928-0.22480.07920.24030.0637-0.4306-0.07790.3955-0.0613-0.00990.43340.00420.3569-22.092617.4372-10.37
45.0003-0.31340.98172.6133-0.70442.9873-0.1466-1.0160.06240.23620.11650.2693-0.0625-0.55980.03750.41770.01350.03370.68120.04480.4138-29.841921.51940.8341
55.9948-1.14131.60580.5604-0.96387.69510.33190.4029-0.7494-0.0976-0.22690.22460.2437-0.7089-0.11610.5906-0.0537-0.05880.6389-0.09320.5162-41.894410.301-29.3493
63.6819-0.50630.60721.6701-0.13471.3414-0.26-0.62570.64650.29740.0868-0.1852-0.1681-0.15320.15570.41060.0502-0.0360.3926-0.12160.5078-0.119528.2824.5224
74.5042-0.87240.63953.4742-0.272.8485-0.0771-1.36180.06040.54430.04590.0314-0.1264-0.30190.05240.50420.07220.02090.6671-0.01780.3128-1.511718.768316.6265
84.43820.1170.42472.0906-0.2141.3314-0.0834-0.01460.1108-0.02440.0301-0.2668-0.01030.21890.0370.35730.0406-0.01030.3152-0.0080.360411.539617.31580.6113
95.36441.1546-0.36475.41824.0173.27390.2450.0889-0.2617-0.2518-0.17410.0428-0.7233-0.41470.08880.6420.0687-0.08330.5030.01950.527224.54339.638117.0469
103.31040.3489-0.0696.01594.49663.39170.0722-0.3522-0.11180.28260.0775-0.10610.6507-0.4579-0.25990.66140.0328-0.07920.67790.0330.540729.01078.664827.3788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 60 through 108 )A60 - 108
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 136 )A109 - 136
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 235 )A137 - 235
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 303 )A236 - 303
5X-RAY DIFFRACTION5chain 'A' and (resid 304 through 358 )A304 - 358
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 108 )B59 - 108
7X-RAY DIFFRACTION7chain 'B' and (resid 109 through 136 )B109 - 136
8X-RAY DIFFRACTION8chain 'B' and (resid 137 through 303 )B137 - 303
9X-RAY DIFFRACTION9chain 'B' and (resid 304 through 318 )B304 - 318
10X-RAY DIFFRACTION10chain 'B' and (resid 319 through 358 )B319 - 358

+
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