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

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Basic information

Entry
Database: PDB / ID: 5gri
TitleCrystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and citrate
Components
  • Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
  • Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
KeywordsOXIDOREDUCTASE / 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 / 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
CITRIC 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: 2.31 Å
AuthorsMa, T. / Peng, Y. / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

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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)75,7905
Polymers75,5502
Non-polymers2413
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-51 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.040, 112.040, 144.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

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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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M sodium citrate, pH 8.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 46471 / % possible obs: 98.4 % / Redundancy: 19.5 % / Net I/σ(I): 53.7
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
HKL-2000data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GRH

5grh


Resolution: 2.31→46.01 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.886 / SU B: 5.499 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2712 2138 5 %RANDOM
Rwork0.2409 ---
obs0.2424 40334 90.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 134.01 Å2 / Biso mean: 44.364 Å2 / Biso min: 7.81 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2--2.09 Å20 Å2
3----4.17 Å2
Refinement stepCycle: final / Resolution: 2.31→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 15 111 5165
Biso mean--21.82 21.72 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195134
X-RAY DIFFRACTIONr_bond_other_d0.0050.025026
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.9626941
X-RAY DIFFRACTIONr_angle_other_deg0.755311556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91724.47217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62415915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1521532
X-RAY DIFFRACTIONr_chiral_restr0.0570.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025801
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021117
LS refinement shellResolution: 2.305→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 37 -
Rwork0.245 469 -
all-506 -
obs--14.79 %

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