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- PDB-8a4k: Human GDAP1, R282H mutant -

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Basic information

Entry
Database: PDB / ID: 8a4k
TitleHuman GDAP1, R282H 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 / protein targeting to mitochondrion / mitochondrial fission / peroxisomal membrane / mitochondrial fusion / response to retinoic acid / mitochondrial outer membrane / mitochondrion / membrane ...Class I peroxisomal membrane protein import / cellular response to vitamin D / protein targeting to mitochondrion / mitochondrial fission / peroxisomal membrane / mitochondrial fusion / response to retinoic acid / mitochondrial outer membrane / mitochondrion / membrane / nucleus / cytosol
Similarity search - Function
Ganglioside-induced differentiation-associated protein 1 / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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: 1.95 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

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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)65,5112
Polymers65,5112
Non-polymers00
Water1,36976
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)73.279, 113.370, 115.194
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 76...
d_2ens_1(chain "B" and (resid 23 through 160 or resid 163 through 281 or resid 283 through 302))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUASNA1 - 50
d_12ens_1GLUILEA54 - 138
d_13ens_1GLNGLNA141
d_14ens_1HISGLUA151 - 181
d_15ens_1GLNGLUA187 - 233
d_16ens_1VALSERA235 - 254
d_21ens_1GLUILEB1 - 135
d_22ens_1GLNGLUB138 - 216
d_23ens_1VALSERB218 - 237

NCS oper: (Code: givenMatrix: (-0.86953374599, 0.492755018954, -0.0332198115481), (0.493812621148, 0.868513827645, -0.0428115216307), (0.0077562735287, -0.0536304249897, -0.99853072949)Vector: 33. ...NCS oper: (Code: given
Matrix: (-0.86953374599, 0.492755018954, -0.0332198115481), (0.493812621148, 0.868513827645, -0.0428115216307), (0.0077562735287, -0.0536304249897, -0.99853072949)
Vector: 33.6433127398, -9.48474933084, -23.6003495359)

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Components

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


Mass: 32755.389 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 / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M succinic acid; 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 70450 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 56.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.053 / Net I/σ(I): 15.4
Reflection shellResolution: 1.95→2.07 Å / Rmerge(I) obs: 2.738 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 11256 / CC1/2: 0.416 / Rrim(I) all: 2.969 / % 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: 1.95→44.84 Å / SU ML: 0.3866 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.1301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251 3770 2.9 %
Rwork0.2247 126355 -
obs0.2254 69656 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 0 76 4142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01424169
X-RAY DIFFRACTIONf_angle_d1.37095645
X-RAY DIFFRACTIONf_chiral_restr0.0686627
X-RAY DIFFRACTIONf_plane_restr0.0159720
X-RAY DIFFRACTIONf_dihedral_angle_d16.05071583
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.42413555888 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.75720.7282430X-RAY DIFFRACTION50.73
1.97-20.55461120.64813890X-RAY DIFFRACTION79.8
2-2.030.55211330.58554499X-RAY DIFFRACTION92.97
2.03-2.060.52411400.54374686X-RAY DIFFRACTION96.52
2.06-2.090.58251470.50974770X-RAY DIFFRACTION97.89
2.09-2.120.45391420.47394762X-RAY DIFFRACTION98.34
2.12-2.160.48361330.43794706X-RAY DIFFRACTION95.52
2.16-2.190.44091410.40254732X-RAY DIFFRACTION98.31
2.19-2.230.42221460.38084840X-RAY DIFFRACTION99.94
2.23-2.280.38011590.35194892X-RAY DIFFRACTION99.78
2.28-2.320.32581490.34594825X-RAY DIFFRACTION99.88
2.32-2.370.37211480.3374836X-RAY DIFFRACTION99.94
2.37-2.430.31821390.28634875X-RAY DIFFRACTION99.9
2.43-2.490.26781490.24434835X-RAY DIFFRACTION99.96
2.49-2.560.20891410.24454848X-RAY DIFFRACTION99.92
2.56-2.630.24061480.23924870X-RAY DIFFRACTION99.94
2.63-2.720.25291440.22464853X-RAY DIFFRACTION99.86
2.72-2.810.28341450.23314901X-RAY DIFFRACTION99.96
2.81-2.920.2311420.24224804X-RAY DIFFRACTION99.88
2.93-3.060.29331500.24544741X-RAY DIFFRACTION96.89
3.06-3.220.27951490.23284748X-RAY DIFFRACTION97.88
3.22-3.420.29591370.23554838X-RAY DIFFRACTION99.9
3.42-3.680.26121300.20164882X-RAY DIFFRACTION99.96
3.68-4.060.2131390.19464852X-RAY DIFFRACTION99.98
4.06-4.640.17581460.16734857X-RAY DIFFRACTION99.94
4.64-5.850.231460.18124825X-RAY DIFFRACTION99.6
5.85-44.840.19741430.18964758X-RAY DIFFRACTION97.63
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)
12.595129643670.1006580742071.134249099590.877212457956-0.1492748612581.48943286130.0432884973399-0.1971510911040.02783419439250.1283626861860.09746216186570.02115211347780.00456506059474-0.2558361267035.47330505017E-50.7587728445470.17742663120.06568531025070.775072336010.1137889081330.7063184299346.961287261270.188958283171-13.855186156
21.90114891826-0.6391357144251.168278693950.876985348597-0.258862583293.26719482640.139815911585-0.269957175406-0.165476070946-0.159366718920.02127093829710.2961899820860.578444419086-0.9364368251817.04411509845E-50.838125947504-0.1279295074030.03093053792990.8924934580140.1771691186730.76110939791-4.56334031581-8.42961040374-26.3565276012
32.87454343329-1.349654149191.922447357791.51775418612-1.062153032361.58449461870.2035301398750.1707678053550.256900100823-0.206519327049-0.188641108274-0.00857590718442-0.307716816877-0.1504737576724.48549316787E-50.6465112838120.06811141398150.07386763255520.6284814686140.04314241918540.64440312251828.0046598168-5.05446243786-8.9377298132
42.343801363370.324711110872-0.1800798929890.838574189408-0.07741954161840.8069162923380.1463691219580.13128891301-0.1798534254350.152318005904-0.2419738422530.147821825585-0.0594309391923-0.2719555855361.14841318668E-50.626941938123-0.05248644019160.01038982059720.669782370886-0.04553375692050.67262714420125.9151990664-21.99730499087.09733030823
52.58901731977-0.1128770149640.05789848803331.75019627452-0.7440956138181.304030777380.170431678803-0.0156800185928-0.1044130649930.161304805031-0.269379007051-0.288051096743-0.01082379919490.298595739782-2.92193085941E-70.598722732106-0.0215345926392-0.01931954783920.585860451601-0.01027156701970.65491970936140.8551619824-14.2360808541.755233718
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 - 92
22chain 'B' and (resid 118 through 302 )BB118 - 30293 - 237
33chain 'A' and (resid 23 through 117 )AA23 - 1171 - 95
44chain 'A' and (resid 118 through 228 )AA118 - 22896 - 180
55chain 'A' and (resid 229 through 302 )AA229 - 302181 - 254

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