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Basic information

Entry
Database: PDB / ID: 8grb
TitleCrystal structure of a constitutively active mutant of the alpha beta heterodimer of human IDH3
Components
  • Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
  • 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
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: 2.848 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 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
C: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
A: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
D: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
E: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
F: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
G: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
H: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
I: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
J: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
K: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
L: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
M: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
N: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
O: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
P: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)606,21716
Polymers606,21716
Non-polymers00
Water00
1
B: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
C: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
A: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
D: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)151,5544
Polymers151,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-82 kcal/mol
Surface area48710 Å2
MethodPISA
2
E: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
F: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
G: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
H: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)151,5544
Polymers151,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-84 kcal/mol
Surface area49150 Å2
MethodPISA
3
I: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
J: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
K: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
L: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)151,5544
Polymers151,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-82 kcal/mol
Surface area48270 Å2
MethodPISA
4
M: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
N: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
O: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
P: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)151,5544
Polymers151,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-87 kcal/mol
Surface area48620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.150, 170.028, 208.692
Angle α, β, γ (deg.)90.00, 103.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial / Isocitric dehydrogenase subunit alpha / NAD(+)-specific ICDH subunit alpha


Mass: 36625.125 Da / Num. of mol.: 8 / Mutation: Q139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH3A / Production host: Escherichia coli (E. coli)
References: UniProt: P50213, isocitrate dehydrogenase (NAD+)
#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.: 8
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

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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 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% (v/v) Tacsimate (pH 7.0) and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / 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: 2.848→50 Å / Num. obs: 165707 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.062 / Rrim(I) all: 0.163 / Χ2: 0.541 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.956.80.737165020.8350.3030.7980.422100
2.95-3.076.60.585165500.8860.2460.6350.443100
3.07-3.2170.452165450.9260.1840.4880.492100
3.21-3.387.10.317164770.1270.3410.482100
3.38-3.5970.222164900.9780.090.240.484100
3.59-3.876.60.157165820.9860.0660.1710.528100
3.87-4.267.20.124165400.9920.050.1340.58100
4.26-4.876.90.096166010.9940.0390.1030.641100
4.87-6.1470.096166550.9940.0390.1040.605100
6.14-506.70.072167650.9970.030.0780.72699.9

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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: 2.848→49.144 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 8371 5.06 %
Rwork0.1988 --
obs0.2013 165392 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.848→49.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39053 0 0 0 39053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01439714
X-RAY DIFFRACTIONf_angle_d1.13353758
X-RAY DIFFRACTIONf_dihedral_angle_d24.66214414
X-RAY DIFFRACTIONf_chiral_restr0.0586229
X-RAY DIFFRACTIONf_plane_restr0.0076994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.848-2.88010.34052940.27135056X-RAY DIFFRACTION96
2.8801-2.91390.34252830.27235190X-RAY DIFFRACTION100
2.9139-2.94950.32162890.26665211X-RAY DIFFRACTION100
2.9495-2.98680.35532680.26525292X-RAY DIFFRACTION100
2.9868-3.02610.36772810.27175196X-RAY DIFFRACTION100
3.0261-3.06760.32542780.26035258X-RAY DIFFRACTION100
3.0676-3.11140.2812810.24385153X-RAY DIFFRACTION100
3.1114-3.15780.28182770.25375265X-RAY DIFFRACTION100
3.1578-3.20710.33993000.25775281X-RAY DIFFRACTION100
3.2071-3.25970.28972920.25425140X-RAY DIFFRACTION100
3.2597-3.31590.3022510.24415281X-RAY DIFFRACTION100
3.3159-3.37620.33062800.24395258X-RAY DIFFRACTION100
3.3762-3.44110.30012840.23245204X-RAY DIFFRACTION100
3.4411-3.51130.28582660.2275238X-RAY DIFFRACTION100
3.5113-3.58770.26952540.22165263X-RAY DIFFRACTION100
3.5877-3.67110.28122810.21495258X-RAY DIFFRACTION100
3.6711-3.76290.24542900.19585227X-RAY DIFFRACTION100
3.7629-3.86460.25222890.18875223X-RAY DIFFRACTION100
3.8646-3.97820.2272960.18755218X-RAY DIFFRACTION100
3.9782-4.10660.24252600.1855269X-RAY DIFFRACTION100
4.1066-4.25330.21642800.17565253X-RAY DIFFRACTION100
4.2533-4.42350.21142920.16385208X-RAY DIFFRACTION100
4.4235-4.62460.19153160.1545241X-RAY DIFFRACTION100
4.6246-4.86830.21232790.15525261X-RAY DIFFRACTION100
4.8683-5.1730.2152730.16765269X-RAY DIFFRACTION100
5.173-5.57190.23222440.18245259X-RAY DIFFRACTION100
5.5719-6.13160.26552710.1955301X-RAY DIFFRACTION100
6.1316-7.01670.22532700.18195244X-RAY DIFFRACTION100
7.0167-8.83190.18282870.15665273X-RAY DIFFRACTION100
8.8319-49.1440.1892650.17345231X-RAY DIFFRACTION97

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