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- PDB-8gs5: Crystal structure of a constitutively active mutant of human IDH3... -

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Basic information

Entry
Database: PDB / ID: 8gs5
TitleCrystal structure of a constitutively active mutant of human IDH3 holoenzyme in apo form
Components
  • Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
  • Isocitrate dehydrogenase [NAD] subunit gamma, 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 / 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
Isoform A of 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: 4.486 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 4, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)605,07916
Polymers605,07916
Non-polymers00
Water00
1
C: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
D: Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
A: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
B: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
G: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
H: Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
E: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
F: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)302,5408
Polymers302,5408
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22830 Å2
ΔGint-180 kcal/mol
Surface area103650 Å2
MethodPISA
2
K: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
L: Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
I: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
J: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
O: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
P: Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
M: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
N: Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)302,5408
Polymers302,5408
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23290 Å2
ΔGint-180 kcal/mol
Surface area102690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.259, 490.331, 330.456
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
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
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.: 4
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
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.: 4
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: 5.33 Å3/Da / Density % sol: 76.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M NaCl, 0.1 M MES (pH 6.5), and 10% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.486→50 Å / Num. obs: 69186 / % possible obs: 89.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.111 / Rrim(I) all: 0.233 / Χ2: 0.903 / Net I/σ(I): 2.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.5-4.6640.80970680.6060.4540.9330.98292.1
4.66-4.8540.6470170.7030.3580.7380.98391.7
4.85-5.0740.57170030.7530.3160.6560.9791.4
5.07-5.334.10.55169900.7530.3020.6320.93490.9
5.33-5.6740.50869360.7660.2820.5850.91590.3
5.67-6.113.80.41969110.7910.2420.4880.88489.5
6.11-6.724.10.29568410.8840.1590.3370.83588.6
6.72-7.694.40.16868720.960.0870.190.83388.6
7.69-9.674.20.09568100.9860.0490.1070.83287.2
9.67-503.90.06767380.9880.0350.0760.87483.3

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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: 7CE3

7ce3


Resolution: 4.486→30.542 Å / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2864 3246 4.97 %
Rwork0.2675 62096 -
obs0.2685 65342 84.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 265.48 Å2 / Biso mean: 107.5421 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 4.486→30.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39351 0 0 0 39351
Num. residues----5370
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.4864-4.55320.32131120.3185212467
4.5532-4.62410.32051100.3167245877
4.6241-4.69960.31341580.3027254081
4.6996-4.78040.28741590.3019254282
4.7804-4.8670.32241350.3097266884
4.867-4.96020.28351300.2974274086
4.9602-5.0610.30581430.3031272687
5.061-5.17050.31331480.2995275187
5.1705-5.29020.35561470.3083276787
5.2902-5.42180.37971580.3137275788
5.4218-5.56750.3461490.3218279188
5.5675-5.73030.30011520.327282388
5.7303-5.9140.33491470.3265278688
5.914-6.12370.35151350.3088281388
6.1237-6.36680.30971510.3169275787
6.3668-6.65370.3571510.3011282688
6.6537-7.00050.28011500.2724283089
7.0005-7.43320.29151330.2553283488
7.4332-7.99760.27711340.2305282487
7.9976-8.7850.23551330.2205282887
8.785-10.01670.19481410.1692278285
10.0167-12.47530.1841590.1604269583
12.4753-30.5420.22511110.2055243472

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