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

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Basic information

Entry
Database: PDB / ID: 8gru
TitleCrystal structure of a constitutively active mutant of the alpha beta heterodimer of human IDH3 in complex with ICT, NAD and Ca
Components
  • Human IDH3 alpha subunit
  • Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, 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 / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix ...isocitrate dehydrogenase complex (NAD+) / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix / magnesium ion binding / mitochondrion / 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
ISOCITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial / Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.847 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 2, 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
Revision 1.3Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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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: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
C: Human IDH3 alpha subunit
D: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,67212
Polymers151,5544
Non-polymers3,1188
Water00
1
A: Human IDH3 alpha subunit
B: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3366
Polymers75,7772
Non-polymers1,5594
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-52 kcal/mol
Surface area24240 Å2
MethodPISA
2
C: Human IDH3 alpha subunit
D: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3366
Polymers75,7772
Non-polymers1,5594
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-52 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.043, 163.833, 163.129
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Human IDH3 alpha subunit


Mass: 36625.125 Da / Num. of mol.: 2 / 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 Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial / Isocitric dehydrogenase subunit beta / NAD(+)-specific ICDH subunit beta


Mass: 39152.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH3B / Production host: Escherichia coli (E. coli) / References: UniProt: O43837-2
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M sodium malonate (pH 6.0), 20% (w/v) PEG 3350, 40 mM ICT, 40 mM NAD and 5 mM Ca2+

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2020
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.847→50 Å / Num. obs: 42112 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.068 / Rrim(I) all: 0.246 / Χ2: 0.665 / Net I/σ(I): 2.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.9511.20.96341440.8360.2931.0070.44799.9
2.95-3.0711.60.87441320.8760.2630.9130.46899.9
3.07-3.2112.90.68242110.920.1940.7090.524100
3.21-3.3813.50.51741420.9550.1440.5370.542100
3.38-3.5913.20.35541700.9750.1010.3690.599100
3.59-3.8712.60.26641960.9820.0780.2780.679100
3.87-4.2613.70.19742130.990.0550.2050.774100
4.26-4.8713.30.14942180.9930.0420.1550.881100
4.87-6.1413.50.1442690.9940.0390.1450.784100
6.14-5012.60.09244170.9990.0270.0960.87599.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KDF

6kdf


Resolution: 2.847→40.958 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 2166 5.16 %
Rwork0.2084 39839 -
obs0.2112 42005 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.22 Å2 / Biso mean: 44.4995 Å2 / Biso min: 14.8 Å2
Refinement stepCycle: final / Resolution: 2.847→40.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9889 0 204 0 10093
Biso mean--53.34 --
Num. residues----1331
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8475-2.91370.35361290.2711243192
2.9137-2.98650.32551480.25892626100
2.9865-3.06720.31641550.26262627100
3.0672-3.15750.30481470.24662654100
3.1575-3.25930.33111480.24872643100
3.2593-3.37580.33661360.24852648100
3.3758-3.51090.30741650.2422649100
3.5109-3.67060.26191400.21982663100
3.6706-3.86390.27451260.2052661100
3.8639-4.10580.22691480.19092684100
4.1058-4.42250.23991450.17712679100
4.4225-4.86690.20031460.1612672100
4.8669-5.56970.2231340.18492724100
5.5697-7.01150.25831460.20622714100
7.0115-40.9580.22981530.1904276498

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