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- PDB-7ce3: Crystal structure of human IDH3 holoenzyme in APO form. -

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Basic information

Entry
Database: PDB / ID: 7ce3
TitleCrystal structure of human IDH3 holoenzyme in APO form.
Components
  • Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
  • Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
  • Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
KeywordsOXIDOREDUCTASE / IDH3 / NAD-IDH / NAD dependent isocitrate dehydrogenase
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 / electron transfer activity / 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
Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial / 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: 3.472 Å
AuthorsSun, P.K. / Ding, J.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31870723 China
CitationJournal: Cell Discov / Year: 2020
Title: Structure and allosteric regulation of human NAD-dependent isocitrate dehydrogenase.
Authors: Sun, P. / Liu, Y. / Ma, T. / Ding, J.
History
DepositionJun 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
B: Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
C: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
D: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)158,3994
Polymers158,3994
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-73 kcal/mol
Surface area52820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.568, 204.568, 237.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial / IDH3 alpha subunit / Isocitric dehydrogenase subunit alpha / NAD(+)-specific ICDH subunit alpha


Mass: 39638.637 Da / Num. of mol.: 2
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 Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial / IDH3 gamma subunit / Isocitric dehydrogenase subunit gamma / NAD(+)-specific ICDH subunit gamma


Mass: 39142.852 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: Protein Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial / IDH3 beta subunit / Isocitric dehydrogenase subunit beta / NAD(+)-specific ICDH subunit beta


Mass: 39978.984 Da / Num. of mol.: 1
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

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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: 3.93 Å3/Da / Density % sol: 68.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.05M NH4Cl, 0.05M Bis-Tris, pH 6.5, 30% pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.47→50 Å / Num. obs: 32854 / % possible obs: 100 % / Redundancy: 17.8 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.025 / Rrim(I) all: 0.105 / Χ2: 0.965 / Net I/σ(I): 8.1 / Num. measured all: 585722
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.47-3.5917.81.87532420.6760.4561.9310.914100
3.59-3.7417.51.16632340.8160.2891.2020.949100
3.74-3.9118.60.93432310.9190.2240.9610.929100
3.91-4.1118.60.55832450.9620.1340.5750.945100
4.11-4.3717.60.33532560.9850.0830.3451100
4.37-4.7118.50.16432520.9960.0390.1681.059100
4.71-5.1818.10.11732780.9980.0280.1210.981100
5.18-5.9317.90.09633020.9980.0230.0990.92100
5.93-7.4717.50.04933360.9990.0120.050.97100
7.47-5016.30.02347810.0050.0210.97899.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KDY

6kdy


Resolution: 3.472→46.339 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 1570 5.14 %
Rwork0.2129 28955 -
obs0.2147 30525 92.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.05 Å2 / Biso mean: 56.0915 Å2 / Biso min: 6.39 Å2
Refinement stepCycle: final / Resolution: 3.472→46.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9853 0 0 0 9853
Num. residues----1338
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.472-3.58350.3634800.284137550
3.5835-3.71160.30271240.2616220479
3.7116-3.86010.27881410.2449266896
3.8601-4.03570.27481470.2372788100
4.0357-4.24830.25011410.21692828100
4.2483-4.51430.24991390.18832798100
4.5143-4.86250.21171640.18252825100
4.8625-5.35120.22341770.20212810100
5.3512-6.1240.29471440.23412832100
6.124-7.70980.23261560.2212879100
7.7098-46.3390.19251570.1766294898

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