[English] 日本語
Yorodumi
- PDB-7b2g: Crystal structure of R120Q GDAP1 mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b2g
TitleCrystal structure of R120Q GDAP1 mutant
ComponentsGanglioside-induced differentiation-associated protein 1
KeywordsSIGNALING PROTEIN / Homodimer / mutant / mitochondria
Function / homology
Function and homology information


Class I peroxisomal membrane protein import / cellular response to vitamin D / mitochondrial fission / peroxisomal membrane / mitochondrial fusion / protein targeting to mitochondrion / response to retinoic acid / mitochondrial outer membrane / mitochondrion / nucleus ...Class I peroxisomal membrane protein import / cellular response to vitamin D / mitochondrial fission / peroxisomal membrane / mitochondrial fusion / protein targeting to mitochondrion / response to retinoic acid / mitochondrial outer membrane / mitochondrion / nucleus / membrane / cytosol
Similarity search - Function
Ganglioside-induced differentiation-associated protein 1 / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Ganglioside-induced differentiation-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNguyen, G.T.T. / Sutinen, A. / Kursula, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: Plos One / Year: 2023
Title: Conserved intramolecular networks in GDAP1 are closely connected to CMT-linked mutations and protein stability.
Authors: Sutinen, A. / Paffenholz, D. / Nguyen, G.T.T. / Ruskamo, S. / Torda, A.E. / Kursula, P.
History
DepositionNov 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: 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.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ganglioside-induced differentiation-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2502
Polymers35,1581
Non-polymers921
Water00
1
A: Ganglioside-induced differentiation-associated protein 1
hetero molecules

A: Ganglioside-induced differentiation-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5004
Polymers70,3162
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1370 Å2
ΔGint-10 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.111, 148.111, 114.538
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

-
Components

#1: Protein Ganglioside-induced differentiation-associated protein 1 / GDAP1


Mass: 35158.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: synthetic construct / Source: (gene. exp.) Homo sapiens (human) / Gene: GDAP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TB36
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.22 Å3/Da / Density % sol: 80.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Succinic acid; 15% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→85.43 Å / Num. obs: 15366 / % possible obs: 99.9 % / Redundancy: 38.5 % / Biso Wilson estimate: 91.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.31
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 1410 / CC1/2: 0.48

-
Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AIA

7aia


Resolution: 3→85.43 Å / SU ML: 0.5719 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2642 1535 10 %
Rwork0.2298 13813 -
obs0.2329 15348 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.64 Å2
Refinement stepCycle: LAST / Resolution: 3→85.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 6 0 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022114
X-RAY DIFFRACTIONf_angle_d0.47962866
X-RAY DIFFRACTIONf_chiral_restr0.0356317
X-RAY DIFFRACTIONf_plane_restr0.002366
X-RAY DIFFRACTIONf_dihedral_angle_d21.6865800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10.55721360.44321224X-RAY DIFFRACTION99.93
3.1-3.210.37331360.39171226X-RAY DIFFRACTION99.93
3.21-3.340.32761360.31871222X-RAY DIFFRACTION100
3.34-3.490.30461370.2931230X-RAY DIFFRACTION99.64
3.49-3.670.2861370.26551237X-RAY DIFFRACTION99.78
3.67-3.90.27991380.25911246X-RAY DIFFRACTION100
3.9-4.20.21491380.20481241X-RAY DIFFRACTION100
4.2-4.630.18981400.1941252X-RAY DIFFRACTION99.93
4.63-5.290.23711400.19721265X-RAY DIFFRACTION99.79
5.3-6.670.2861430.2231283X-RAY DIFFRACTION99.93
6.67-85.430.24731540.19171387X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: 64.5370048195 Å / Origin y: -16.8249563556 Å / Origin z: 9.90204819568 Å
111213212223313233
T0.935973104543 Å20.17867134432 Å2-0.0317857165307 Å2-0.621648271139 Å20.000891157680746 Å2--0.721674998842 Å2
L2.50157469911 °20.737460641076 °2-0.164093431449 °2-3.91763224831 °2-0.498285476524 °2--4.31870601901 °2
S-0.0643744641543 Å °-0.125587998969 Å °-0.0204913756528 Å °-0.189390818595 Å °0.0314432690739 Å °0.232874717415 Å °-0.684228887233 Å °-0.374158943828 Å °0.0248662019802 Å °
Refinement TLS groupSelection details: all

+
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