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- PDB-6ke3: Crystal structure of the alpha bata heterodimer of human IDH3 in ... -

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Basic information

Entry
Database: PDB / ID: 6ke3
TitleCrystal structure of the alpha bata heterodimer of human IDH3 in complex with NADH
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 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: 3.307 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 3, 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
B: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
C: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,78212
Polymers306,1208
Non-polymers2,6624
Water00
1
A: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
B: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1953
Polymers76,5302
Non-polymers6651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-37 kcal/mol
Surface area24880 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
D: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1953
Polymers76,5302
Non-polymers6651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-33 kcal/mol
Surface area24720 Å2
MethodPISA
3
E: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
F: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1953
Polymers76,5302
Non-polymers6651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-33 kcal/mol
Surface area24740 Å2
MethodPISA
4
G: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
H: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1953
Polymers76,5302
Non-polymers6651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-36 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.365, 162.669, 114.776
Angle α, β, γ (deg.)90.000, 100.380, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4
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.: 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
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.09 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.05M a-KG,0.05M NADH, 0.2 M calcium acetate (pH 7.5) 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: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 48488 / % possible obs: 91.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.06 / Rrim(I) all: 0.128 / Χ2: 1.433 / Net I/σ(I): 7.9 / Num. measured all: 211050
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.424.60.54147750.7840.2790.6130.53189.9
3.42-3.554.40.4447440.8690.2310.50.64590.5
3.55-3.723.60.18931600.9870.1150.2242.28559.7
3.72-3.914.50.27347200.9220.1440.3111.20189.2
3.91-4.164.30.16650170.9720.0860.1881.13694.8
4.16-4.484.30.11851960.9830.060.1331.38897.8
4.48-4.934.40.09751600.990.0480.1091.74997.3
4.93-5.644.30.09351440.9890.0470.1051.7396.7
5.64-7.14.60.0852970.9920.040.091.75199.4
7.1-504.30.04952750.9960.0270.0562.23397.6

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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 / Resolution: 3.307→42.164 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2994 2292 4.8 %
Rwork0.2504 45452 -
obs0.2527 47744 89.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 250.53 Å2 / Biso mean: 60.0158 Å2 / Biso min: 19.42 Å2
Refinement stepCycle: final / Resolution: 3.307→42.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19055 0 176 0 19231
Biso mean--79.29 --
Num. residues----2650
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3073-3.37920.41311020.4112235173
3.3792-3.45780.40171380.3729286290
3.4578-3.54420.39281440.3532286090
3.5442-3.640.62661000.4661196862
3.64-3.7470.62041020.5105168253
3.747-3.86790.34631520.3368296694
3.8679-4.0060.37921420.2928265684
4.006-4.16630.27881600.2259306696
4.1663-4.35570.23171560.2099309398
4.3557-4.58510.2931630.1953312498
4.5851-4.8720.21821740.1821306997
4.872-5.24750.24661780.1888312198
5.2475-5.77440.25131360.2111308997
5.7744-6.60720.23581590.2147318199
6.6072-8.31390.24311460.20543215100
8.3139-42.1640.23161400.1998314996

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