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

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Basic information

Entry
Database: PDB / ID: 5gre
TitleCrystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+), citrate and ADP
Components(Isocitrate dehydrogenase [NAD] subunit ...) x 2
KeywordsOXIDOREDUCTASE / CIT / ADP / 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
ADENOSINE-5'-DIPHOSPHATE / 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: 2.65 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

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
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-58 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.910, 104.910, 146.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Isocitrate dehydrogenase [NAD] subunit ... , 2 types, 2 molecules AB

#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+)

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Non-polymers , 4 types, 62 molecules

#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-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.08 Å3/Da / Density % sol: 60 %
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: 2.65→50 Å / Num. obs: 27500 / % possible obs: 99.9 % / Redundancy: 9.1 % / Net I/σ(I): 22.4
Reflection shellResolution: 2.65→2.74 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: 2.65→45.43 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.616 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.061
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 1382 5 %RANDOM
Rwork0.1947 ---
obs0.1971 26073 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.6 Å2 / Biso mean: 49.333 Å2 / Biso min: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1-3.69 Å20 Å20 Å2
2--3.69 Å20 Å2
3----7.39 Å2
Refinement stepCycle: final / Resolution: 2.65→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 42 58 5142
Biso mean--35.95 31.65 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195175
X-RAY DIFFRACTIONr_bond_other_d0.0070.025044
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9697003
X-RAY DIFFRACTIONr_angle_other_deg1.01311602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.22624.495218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33915917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5681532
X-RAY DIFFRACTIONr_chiral_restr0.0810.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215826
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021121
X-RAY DIFFRACTIONr_mcbond_it4.7094.7572636
X-RAY DIFFRACTIONr_mcbond_other4.6794.7542635
X-RAY DIFFRACTIONr_mcangle_it6.8777.1213288
LS refinement shellResolution: 2.653→2.722 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 89 -
Rwork0.251 1885 -
all-1974 -
obs--98.7 %

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