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- PDB-5grl: Crystal structure of the alpha gamma heterodimer of human IDH3 in... -

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Basic information

Entry
Database: PDB / ID: 5grl
TitleCrystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+), isocitrate and ADP
Components
  • Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
  • Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
KeywordsOXIDOREDUCTASE / allosteric regulation / 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 / mitochondrial matrix / nucleolus / magnesium ion binding / mitochondrion / ATP binding / 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
ADENOSINE-5'-DIPHOSPHATE / ISOCITRIC ACID / 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: 2.79 Å
AuthorsMa, T. / Ding, J.
Funding support China, 3items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31170690 China
the Ministry of Science and Technology of China2011CB911102 China
the Chinese Academy of SciencesXDB08010302 China
CitationJournal: Sci Rep / Year: 2017
Title: Molecular mechanism of the allosteric regulation of the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.
Authors: Ma, T. / Peng, Y. / Huang, W. / Ding, J.
History
DepositionAug 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2186
Polymers75,5502
Non-polymers6684
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-56 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.238, 111.238, 145.478
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 36682.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH3A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P50213, isocitrate dehydrogenase (NAD+)
#2: Protein Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial / Isocitric dehydrogenase subunit gamma / NAD(+)-specific ICDH subunit gamma


Mass: 38867.523 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P51553, isocitrate dehydrogenase (NAD+)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7

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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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES-Na, pH 7.5, 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 25878 / % possible obs: 98.1 % / Redundancy: 2.8 % / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GRI

5gri


Resolution: 2.79→50 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.851 / SU B: 15.599 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.748 / ESU R Free: 0.361
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 1284 5 %RANDOM
Rwork0.2262 ---
obs0.2286 24151 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.92 Å2 / Biso mean: 39.353 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 2.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5035 0 42 0 5077
Biso mean--22.34 --
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195154
X-RAY DIFFRACTIONr_bond_other_d0.0060.025025
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9686971
X-RAY DIFFRACTIONr_angle_other_deg0.88311555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7035653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08824.47217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66315913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8441532
X-RAY DIFFRACTIONr_chiral_restr0.0570.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021119
X-RAY DIFFRACTIONr_mcbond_it2.2673.8982627
X-RAY DIFFRACTIONr_mcbond_other2.2623.8972626
X-RAY DIFFRACTIONr_mcangle_it3.6545.8273275
LS refinement shellResolution: 2.794→2.866 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 73 -
Rwork0.319 1419 -
all-1492 -
obs--77.75 %

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