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- PDB-6kdf: Crystal structure of the alpha beta heterodimer of human IDH3 in ... -

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Basic information

Entry
Database: PDB / ID: 6kdf
TitleCrystal structure of the alpha beta heterodimer of human IDH3 in APO form.
Components
  • Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
  • Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
KeywordsOXIDOREDUCTASE / 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 / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity ...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 / electron transfer activity / mitochondrial matrix / magnesium ion binding / mitochondrion / nucleus
Similarity search - Function
Isocitrate dehydrogenase NAD-dependent / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
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: 3.05 Å
AuthorsSun, P. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Molecular basis for the function of the alpha beta heterodimer of human NAD-dependent isocitrate dehydrogenase.
Authors: Sun, P. / Ma, T. / Zhang, T. / Zhu, H. / Zhang, J. / Liu, Y. / Ding, J.
History
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)612,24016
Polymers612,24016
Non-polymers00
Water00
1
B: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
C: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)76,5302
Polymers76,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-33 kcal/mol
Surface area25610 Å2
MethodPISA
2
A: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
D: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)76,5302
Polymers76,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-33 kcal/mol
Surface area25000 Å2
MethodPISA
3
E: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
F: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)76,5302
Polymers76,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-34 kcal/mol
Surface area25730 Å2
MethodPISA
4
G: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
H: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)76,5302
Polymers76,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-33 kcal/mol
Surface area25470 Å2
MethodPISA
5
I: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
J: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)76,5302
Polymers76,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-33 kcal/mol
Surface area25290 Å2
MethodPISA
6
K: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
L: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)76,5302
Polymers76,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-31 kcal/mol
Surface area25000 Å2
MethodPISA
7
M: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
N: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)76,5302
Polymers76,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-34 kcal/mol
Surface area25480 Å2
MethodPISA
8
O: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
P: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)76,5302
Polymers76,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-34 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.913, 170.434, 208.094
Angle α, β, γ (deg.)90.000, 103.430, 90.000
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: 36826.305 Da / Num. of mol.: 8
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 beta, mitochondrial / Isocitric dehydrogenase subunit beta / NAD(+)-specific ICDH subunit beta


Mass: 39703.664 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
Sequence detailsTHIS SEQUENCE OF IDH3 B CORRESPONDS TO THE A ISOFORM FOUND IN UNP 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: 3.15 Å3/Da / Density % sol: 60.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 8% (v/v) tacsimate (pH 6.0) and 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 134178 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.055 / Rrim(I) all: 0.145 / Χ2: 0.936 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.06-3.176.31.04133230.6280.4511.1360.91699.9
3.17-3.370.725134370.8130.2950.7830.894100
3.3-3.457.10.495133500.8990.1990.5340.907100
3.45-3.637.10.335133730.9480.1350.3610.939100
3.63-3.8670.217134280.9760.0880.2350.987100
3.86-4.156.50.155133480.9840.0660.1691.03599.9
4.15-4.577.10.098134250.9940.040.1061.05100
4.57-5.237.10.075134570.9950.030.0811.008100
5.23-6.596.60.07134470.9950.0290.0760.82399.8
6.59-506.80.048135900.9980.020.0520.79299.8

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Processing

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

6kde


Resolution: 3.05→49.75 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.88
RfactorNum. reflection% reflection
Rfree0.2271 6593 5.02 %
Rwork0.1773 --
obs0.1798 131272 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.15 Å2 / Biso mean: 55.2362 Å2 / Biso min: 16.99 Å2
Refinement stepCycle: final / Resolution: 3.05→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39059 0 0 0 39059
Num. residues----5218
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0505-3.08510.36941480.2918303472
3.0851-3.12140.30861680.2825345581
3.1214-3.15950.3311840.2729372187
3.1595-3.19950.35012100.2677405995
3.1995-3.24160.32422130.25416898
3.2416-3.2860.28752370.2469426599
3.286-3.33290.31562500.24574138100
3.3329-3.38260.32942280.24144237100
3.3826-3.43550.30552270.23194212100
3.4355-3.49180.29072330.21474223100
3.4918-3.5520.26082040.20144291100
3.552-3.61650.24852100.19684211100
3.6165-3.68610.26082530.19174233100
3.6861-3.76130.21332090.18994273100
3.7613-3.84310.24672120.18094294100
3.8431-3.93240.23382480.17564193100
3.9324-4.03070.24932220.17314267100
4.0307-4.13960.22522100.16694274100
4.1396-4.26140.21432530.16274227100
4.2614-4.39890.19652200.14454256100
4.3989-4.5560.20512280.14554255100
4.556-4.73830.17662140.13374282100
4.7383-4.95370.16972380.13964250100
4.9537-5.21460.19672210.14924298100
5.2146-5.54090.22952110.15964261100
5.5409-5.96810.23432480.17414255100
5.9681-6.56750.21462260.16734272100
6.5675-7.5150.18592430.14934287100
7.515-9.45750.15412300.13874289100
9.4575-49.750.19081950.1669419995

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