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- PDB-8grh: Crystal structure of a constitutively active mutant of the alpha ... -

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Basic information

Entry
Database: PDB / ID: 8grh
TitleCrystal structure of a constitutively active mutant of the alpha gamma heterodimer of human IDH3 in complex with CIT
Components
  • Human IDH3 alpha subunit
  • Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
KeywordsOXIDOREDUCTASE / Isocitrate dehydrogenase / NAD-dependent IDH / assembly / allosteric regulation
Function / homology
Function and homology information


isocitrate dehydrogenase complex (NAD+) / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process ...isocitrate dehydrogenase complex (NAD+) / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix / nucleolus / magnesium ion binding / mitochondrion / ATP binding / nucleus
Similarity search - Function
Isocitrate dehydrogenase NAD-dependent / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase
Similarity search - Domain/homology
CITRIC ACID / Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial / Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 Å
AuthorsSun, P. / Chen, X. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870723 China
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structures of a constitutively active mutant of human IDH3 reveal new insights into the mechanisms of allosteric activation and the catalytic reaction.
Authors: Chen, X. / Sun, P. / Liu, Y. / Shen, S. / Ma, T. / Ding, J.
History
DepositionSep 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: 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: Human IDH3 alpha subunit
B: Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6853
Polymers75,4932
Non-polymers1921
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-30 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.992, 111.992, 145.925
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Human IDH3 alpha subunit


Mass: 36625.125 Da / Num. of mol.: 1 / Mutation: Q139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P50213
#2: Protein Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial / NAD-IDH gamma subunit / Isocitric dehydrogenase subunit gamma / NAD(+)-specific ICDH subunit gamma


Mass: 38867.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH3G / Production host: Escherichia coli (E. coli) / References: UniProt: P51553
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.5 Å3/Da / Density % sol: 64.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.02 M citric acid, 0.08 M Bis-tris propane (pH 8.8) and 16% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2017
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 36769 / % possible obs: 99.7 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.029 / Rrim(I) all: 0.127 / Χ2: 0.709 / Net I/σ(I): 3.5 / Num. measured all: 703070
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5913.40.75735500.9530.1980.7850.49897.4
2.59-2.6918.70.88336260.9670.2070.9070.488100
2.69-2.8220.60.70936360.980.160.7270.506100
2.82-2.9620.30.50336390.9870.1150.5160.538100
2.96-3.15190.33636450.9930.0790.3450.595100
3.15-3.3920.70.22336900.9970.0510.2290.695100
3.39-3.7320.50.15336750.9970.0350.1570.846100
3.73-4.2719.40.10936950.9980.0250.1121.004100
4.27-5.3820.50.08137300.9990.0180.0831.035100
5.38-50180.05438830.9990.0130.0560.782100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GRH

5grh


Resolution: 2.506→48.642 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1844 5.07 %
Rwork0.2168 34554 -
obs0.219 36398 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.79 Å2 / Biso mean: 79.0779 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.506→48.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 13 33 5085
Biso mean--67.6 74.83 -
Num. residues----659
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.506-2.57340.40931350.3866243993
2.5734-2.64910.43231250.3475263799
2.6491-2.73460.40761460.3087266199
2.7346-2.83240.3071640.2732259499
2.8324-2.94580.33131280.2764269099
2.9458-3.07980.27251340.2636264199
3.0798-3.24220.36861420.25732670100
3.2422-3.44520.2931480.23632670100
3.4452-3.71120.25331300.22092701100
3.7112-4.08450.241390.20412697100
4.0845-4.67510.19771400.17832734100
4.6751-5.88850.21271660.18892711100
5.8885-48.6420.23921470.1789270995

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