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- PDB-8a4j: Human GDAP1, A247V mutant -

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Basic information

Entry
Database: PDB / ID: 8a4j
TitleHuman GDAP1, A247V mutant
ComponentsGanglioside-induced differentiation-associated protein 1
KeywordsMEMBRANE PROTEIN / GST family / mitochondria / disease mutation / dimer
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: 2.68 Å
AuthorsSutinen, A. / Kursula, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland24302881 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
DepositionJun 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ganglioside-induced differentiation-associated protein 1
B: Ganglioside-induced differentiation-associated protein 1


Theoretical massNumber of molelcules
Total (without water)65,6052
Polymers65,6052
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.288, 115.688, 115.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 23 through 72 or resid 77...
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUASNA1 - 50
d_12ens_1VALILEA52 - 135
d_13ens_1ARGARGA138
d_14ens_1SERSERA141
d_15ens_1ASPGLUA147 - 175
d_16ens_1GLNSERA183 - 249
d_21ens_1GLUSERB1 - 232

NCS oper: (Code: givenMatrix: (-0.848031280417, 0.528413984447, -0.0402692000905), (0.529608319266, 0.847753273135, -0.0287995842625), (0.0189202431127, -0.0457498516957, -0.998773735873)Vector: 33. ...NCS oper: (Code: given
Matrix: (-0.848031280417, 0.528413984447, -0.0402692000905), (0.529608319266, 0.847753273135, -0.0287995842625), (0.0189202431127, -0.0457498516957, -0.998773735873)
Vector: 33.4162701025, -10.356043877, -23.559160743)

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Components

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


Mass: 32802.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TB36
#2: Water ChemComp-HOH / water


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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.15 M DL-malic acid (pH 7.3), 20% (w/v) PEG3500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 28237 / % possible obs: 99.7 % / Redundancy: 13.1 % / Biso Wilson estimate: 85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.091 / Net I/σ(I): 16.9
Reflection shellResolution: 2.68→2.84 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.627 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 4457 / CC1/2: 0.814 / Rrim(I) all: 169 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ALM

7alm


Resolution: 2.68→42.28 Å / SU ML: 0.4873 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2838 1998 7.08 %
Rwork0.2518 26207 -
obs0.2541 28205 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.42 Å2
Refinement stepCycle: LAST / Resolution: 2.68→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 0 11 4004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154080
X-RAY DIFFRACTIONf_angle_d1.44935520
X-RAY DIFFRACTIONf_chiral_restr0.0743618
X-RAY DIFFRACTIONf_plane_restr0.0133699
X-RAY DIFFRACTIONf_dihedral_angle_d14.42391554
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.87068764288 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.750.52231430.54891819X-RAY DIFFRACTION98.59
2.75-2.820.46371400.44831860X-RAY DIFFRACTION99.7
2.82-2.910.361380.36631815X-RAY DIFFRACTION100
2.91-30.35231400.31141838X-RAY DIFFRACTION99.95
3-3.110.29251430.26181877X-RAY DIFFRACTION99.9
3.11-3.230.27621450.25351859X-RAY DIFFRACTION99.36
3.23-3.380.27751390.2571824X-RAY DIFFRACTION99.29
3.38-3.560.34641450.27691857X-RAY DIFFRACTION99.65
3.56-3.780.26391380.22511866X-RAY DIFFRACTION99.8
3.78-4.070.33191410.23231898X-RAY DIFFRACTION99.85
4.07-4.480.25611420.23081871X-RAY DIFFRACTION99.85
4.48-5.130.2711460.21531880X-RAY DIFFRACTION99.17
5.13-6.450.30981450.26561942X-RAY DIFFRACTION99.95
6.46-42.280.2311530.23532001X-RAY DIFFRACTION99.26
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)
17.59935060281-0.394888157598-0.5809529081432.333318112650.5688589000377.838721709940.0761232111731-0.1698458711680.3552660300270.152560379737-0.08669643626280.136911960152-0.329801876743-0.3556202585740.04348370270630.7565377295010.1698480869460.04893074585340.9387706798980.1526670616610.866543978226.974610558540.329970743474-13.5358684645
25.44242069532-1.28032457561-1.638975750862.15791550614-0.6741199019557.93866648987-0.00951521926734-0.295705732412-0.165636374186-0.3841852299430.08351572775720.5205089189811.01421656726-1.303313732830.003989748248490.726580168238-0.255783025769-0.06574317682680.8277628670140.1115813811010.674819219825-4.86343866726-7.90138349726-26.3166056906
37.68087026247-4.781070858060.3734225296636.716432146151.51781752346.867204185340.1317108184840.07513667197870.382134510056-0.3229810041060.000705028191912-0.184082210772-0.2522945877360.258778969553-0.1456158962650.393581199574-0.02478455253120.01886040187960.6893117558810.05973813734590.65088692840628.2495926917-5.29359983947-9.0220308458
46.68667088513-0.479431344305-3.38361079071.617566998660.366936078415.51597825857-0.117236989252-0.1264303253620.1193280608340.22309396690.228368088752-0.00571540412935-0.3056420153340.5248414884450.156849040370.576720275488-0.0129015444713-0.02751016868590.865047502792-0.003078329831280.79446189832326.214071242-17.86810295766.12128100389
57.133953364050.111813268182-1.971339682292.39155305922-0.3736385596293.138394441490.0723937187258-0.301272398597-0.4798546879110.110735215439-0.317607916013-0.1850562068780.1599863099890.2720112068690.1948353177480.4512631238720.00022711180586-0.03859672845590.699381754774-0.01851827877120.59692969511635.680252561-18.9783366553.9934504766
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 23 through 117 )BB23 - 1171 - 91
22chain 'B' and (resid 118 through 302 )BB118 - 30292 - 232
33chain 'A' and (resid 23 through 117 )AA23 - 1171 - 92
44chain 'A' and (resid 118 through 189 )AA118 - 18993 - 136
55chain 'A' and (resid 190 through 302 )AA190 - 302137 - 249

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