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- PDB-7q6j: Crystal structure of the human GDAP1 CMT2 mutant-H123R -

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Basic information

Entry
Database: PDB / ID: 7q6j
TitleCrystal structure of the human GDAP1 CMT2 mutant-H123R
ComponentsGanglioside-induced differentiation-associated protein 1
KeywordsSIGNALING PROTEIN / Charcot-Marie-Tooth / CMT2 / Mutation / Mitochondria
Function / homology
Function and homology information


Class I peroxisomal membrane protein import / cellular response to vitamin D / protein targeting to mitochondrion / mitochondrial fission / mitochondrial fusion / peroxisomal membrane / 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 / mitochondrial fusion / peroxisomal membrane / response to retinoic acid / mitochondrial outer membrane / mitochondrion / membrane / nucleus / 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
DI(HYDROXYETHYL)ETHER / Ganglioside-induced differentiation-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSutinen, A. / Kursula, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland24302881 Finland
CitationJournal: Febs Open Bio / Year: 2022
Title: Structural insights into Charcot-Marie-Tooth disease-linked mutations in human GDAP1.
Authors: Sutinen, A. / Nguyen, G.T.T. / Raasakka, A. / Muruganandam, G. / Loris, R. / Ylikallio, E. / Tyynismaa, H. / Bartesaghi, L. / Ruskamo, S. / Kursula, P.
History
DepositionNov 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7994
Polymers65,5872
Non-polymers2122
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-9 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.710, 115.880, 116.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 23 through 30 or resid 32...
21(chain B and (resid 23 through 30 or resid 32...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUHISHIS(chain A and (resid 23 through 30 or resid 32...AA23 - 301 - 8
12THRTHRPHEPHE(chain A and (resid 23 through 30 or resid 32...AA32 - 3510 - 13
13SERSERVALVAL(chain A and (resid 23 through 30 or resid 32...AA37 - 4015 - 18
14LEULEUHISHIS(chain A and (resid 23 through 30 or resid 32...AA42 - 6320 - 41
15GLUGLUSERSER(chain A and (resid 23 through 30 or resid 32...AA23 - 3021 - 280
16GLUGLUSERSER(chain A and (resid 23 through 30 or resid 32...AA23 - 3021 - 280
17LEULEUGLNGLN(chain A and (resid 23 through 30 or resid 32...AA197 - 224175 - 202
18GLUGLUSERSER(chain A and (resid 23 through 30 or resid 32...AA23 - 3021 - 280
19ARGARGSERSER(chain A and (resid 23 through 30 or resid 32...AA226 - 302204 - 280
21GLUGLUHISHIS(chain B and (resid 23 through 30 or resid 32...BB23 - 301 - 8
22THRTHRPHEPHE(chain B and (resid 23 through 30 or resid 32...BB32 - 3510 - 13
23SERSERVALVAL(chain B and (resid 23 through 30 or resid 32...BB37 - 4015 - 18
24GLYGLYSERSER(chain B and (resid 23 through 30 or resid 32...BB139 - 162117 - 140
25GLUGLUSERSER(chain B and (resid 23 through 30 or resid 32...BB23 - 3021 - 280
26LEULEUGLNGLN(chain B and (resid 23 through 30 or resid 32...BB197 - 224175 - 202
27GLUGLUSERSER(chain B and (resid 23 through 30 or resid 32...BB23 - 3021 - 280
28ARGARGSERSER(chain B and (resid 23 through 30 or resid 32...BB226 - 302204 - 280

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Components

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


Mass: 32793.484 Da / Num. of mol.: 2 / Mutation: H123R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDAP1 / Plasmid: pTH-27 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TB36
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, DL-Malic Acid

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2019
RadiationMonochromator: double crystal silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→45.38 Å / Num. obs: 50431 / % possible obs: 99.8 % / Redundancy: 6.515 % / Biso Wilson estimate: 59.891 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.079 / Χ2: 0.851 / Net I/σ(I): 14.78 / Num. measured all: 328536 / Scaling rejects: 288
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.266.661.6021.4324288367936470.751.73899.1
2.26-2.326.8091.3911.7524506361635990.8011.50699.5
2.32-2.396.7970.9642.4423618347934750.8651.04599.9
2.39-2.466.6990.8012.9922711339333900.8990.86999.9
2.46-2.546.3440.6473.6620947330333020.9240.705100
2.54-2.636.6320.4994.7621243320532030.9530.54299.9
2.63-2.736.4730.3886.0819846307330660.9660.42299.8
2.73-2.846.8750.2678.2620440297829730.9820.28999.8
2.84-2.976.8690.20110.5119612285528550.990.217100
2.97-3.116.7490.14413.5718451273427340.9940.156100
3.11-3.286.3750.10117.2516625261026080.9970.1199.9
3.28-3.486.4740.07221.6215985247124690.9980.07899.9
3.48-3.726.5310.05327.515264233823370.9990.057100
3.72-4.026.50.04630.2914184218221820.9990.05100
4.02-4.46.2540.03935.0212520200520020.9990.04299.9
4.4-4.925.7450.03836.0410496183118270.9980.04299.8
4.92-5.685.8930.03737.229564162716230.9980.0499.8
5.68-6.966.0930.03241.158493139713940.9990.03599.8
6.96-9.845.5660.02650.636150110811050.9990.02899.7
9.84-45.385.6140.0261.2235936506400.9990.02298.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.2 Å45.38 Å
Translation2.2 Å45.38 Å

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Processing

Software
NameVersionClassification
XDSFeb 5, 2021data reduction
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.18-3861refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ALM

7alm


Resolution: 2.2→45.38 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1990 3.95 %
Rwork0.2153 48411 -
obs0.2162 50401 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 264.71 Å2 / Biso mean: 81.1917 Å2 / Biso min: 31.83 Å2
Refinement stepCycle: final / Resolution: 2.2→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 34 93 4299
Biso mean--78.38 56.84 -
Num. residues----505
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2313X-RAY DIFFRACTION15.07TORSIONAL
12B2313X-RAY DIFFRACTION15.07TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.41321400.39853359349999
2.26-2.320.33611370.32943406354399
2.32-2.380.32621390.282334143553100
2.38-2.460.30321420.266634043546100
2.46-2.550.29151440.24134393583100
2.55-2.650.2731400.241634313571100
2.65-2.770.29491420.248234283570100
2.77-2.920.28311420.262334473589100
2.92-3.10.28731420.238534533595100
3.1-3.340.24211440.225734603604100
3.34-3.680.24481410.216834563597100
3.68-4.210.18221440.192935013645100
4.21-5.30.19221460.171535413687100
5.3-45.380.21711470.194936723819100
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)
11.9168-1.30760.97491.1346-0.65070.76260.12-0.2397-0.14420.1842-0.0812-0.10720.0694-0.081200.4682-0.0243-0.0490.4810.01960.4268-9.4888-37.386723.7586
21.68520.26-0.03191.2080.39111.19020.14740.0980.0321-0.01710.04210.0121-0.1286-0.049200.40230.0330.01440.4209-0.02090.3478-13.7703-23.831910.0108
31.8057-1.31770.31121.275-0.64770.6532-0.0331-0.09980.0502-0.2561-0.0298-0.4723-0.0083-0.0623-0.00050.4286-0.0258-0.08140.38930.09180.511510.3481-43.359229.7313
40.5991-0.14890.10220.2588-0.2970.35820.29640.27640.6076-1.3446-0.4944-0.52860.240.2533-0.11341.03160.120.32820.68810.24720.798520.5818-52.935117.8362
50.866-1.13920.03081.6079-0.44720.79470.08990.55990.6871-0.6932-0.222-1.03960.35050.5014-0.00910.83580.11270.44820.58130.27020.962925.636-54.41718.5558
60.5652-0.69380.43190.9638-0.39370.276-0.065-0.17550.3012-0.2076-0.0818-1.31250.10490.25-0.02440.5427-0.00970.19060.53090.16690.922524.2695-55.97927.9234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 117 )A23 - 117
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 302 )A118 - 302
3X-RAY DIFFRACTION3chain 'B' and (resid 23 through 115 )B23 - 115
4X-RAY DIFFRACTION4chain 'B' and (resid 116 through 153 )B116 - 153
5X-RAY DIFFRACTION5chain 'B' and (resid 154 through 245 )B154 - 245
6X-RAY DIFFRACTION6chain 'B' and (resid 246 through 302 )B246 - 302

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