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- PDB-7p0o: mitoNEET bound to M1 molecule -

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Basic information

Entry
Database: PDB / ID: 7p0o
TitlemitoNEET bound to M1 molecule
ComponentsCDGSH iron-sulfur domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / [2Fe-2S] proteins / NEET proteins / destabilizer / M1
Function / homology
Function and homology information


protein maturation by [2Fe-2S] cluster transfer / cysteine transaminase / L-cysteine transaminase activity / regulation of cellular respiration / regulation of autophagy / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial outer membrane / protein homodimerization activity / mitochondrion ...protein maturation by [2Fe-2S] cluster transfer / cysteine transaminase / L-cysteine transaminase activity / regulation of cellular respiration / regulation of autophagy / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial outer membrane / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding
Similarity search - Function
Iron sulphur domain-containing, mitoNEET, N-terminal / Iron-containing outer mitochondrial membrane protein N-terminus / CDGSH iron-sulfur domain-containing protein 1/2 / Iron-binding zinc finger CDGSH type / Iron-binding zinc finger, CDGSH type / MitoNEET, CDGSH iron-sulfur domain / CDGSH-type zinc finger. Function unknown.
Similarity search - Domain/homology
Chem-49I / Chem-4OY / FE2/S2 (INORGANIC) CLUSTER / CDGSH iron-sulfur domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLivnah, O. / Eisenberg-Domovich, Y. / Marjault, H.B. / Nechushtai, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN765048 Israel
CitationJournal: Commun Biol / Year: 2022
Title: An anti-diabetic drug targets NEET (CISD) proteins through destabilization of their [2Fe-2S] clusters.
Authors: Marjault, H.B. / Karmi, O. / Zuo, K. / Michaeli, D. / Eisenberg-Domovich, Y. / Rossetti, G. / de Chassey, B. / Vonderscher, J. / Cabantchik, I. / Carloni, P. / Mittler, R. / Livnah, O. / ...Authors: Marjault, H.B. / Karmi, O. / Zuo, K. / Michaeli, D. / Eisenberg-Domovich, Y. / Rossetti, G. / de Chassey, B. / Vonderscher, J. / Cabantchik, I. / Carloni, P. / Mittler, R. / Livnah, O. / Meldrum, E. / Nechushtai, R.
History
DepositionJun 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CDGSH iron-sulfur domain-containing protein 1
B: CDGSH iron-sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0036
Polymers17,8972
Non-polymers1,1074
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-50 kcal/mol
Surface area7380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.152, 49.962, 58.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CDGSH iron-sulfur domain-containing protein 1 / MitoNEET


Mass: 8948.327 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CISD1, C10orf70, ZCD1, MDS029 / Plasmid: pet21a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9NZ45
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-49I / 2-benzamido-4-[(2~{R})-1,2,3,4-tetrahydronaphthalen-2-yl]thiophene-3-carboxylic acid


Mass: 377.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-4OY / 2-benzamido-4-[(2~{S})-1,2,3,4-tetrahydronaphthalen-2-yl]thiophene-3-carboxylic acid


Mass: 377.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19NO3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 32% PEG-3000, 100 mM Tris-HCl (pH 8.0) and100mM NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 1M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.65→45.15 Å / Num. obs: 15754 / % possible obs: 99.69 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.2
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.0188 / Num. unique obs: 1151

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EW0

3ew0


Resolution: 1.65→38.11 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.957 / SU B: 8.558 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23645 805 4.9 %RANDOM
Rwork0.1711 ---
obs0.17435 15754 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.553 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2--2.49 Å2-0 Å2
3----4.57 Å2
Refinement stepCycle: 1 / Resolution: 1.65→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 0 62 50 1175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191155
X-RAY DIFFRACTIONr_bond_other_d0.0030.021094
X-RAY DIFFRACTIONr_angle_refined_deg2.191.9951545
X-RAY DIFFRACTIONr_angle_other_deg0.97632534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.2862552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20215211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.428154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021264
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02270
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7923.449526
X-RAY DIFFRACTIONr_mcbond_other3.7253.445525
X-RAY DIFFRACTIONr_mcangle_it4.7075.16654
X-RAY DIFFRACTIONr_mcangle_other4.7045.165655
X-RAY DIFFRACTIONr_scbond_it4.5833.98629
X-RAY DIFFRACTIONr_scbond_other4.5813.981630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8435.798888
X-RAY DIFFRACTIONr_long_range_B_refined6.44341.5771263
X-RAY DIFFRACTIONr_long_range_B_other6.37941.4821260
X-RAY DIFFRACTIONr_rigid_bond_restr2.40332249
X-RAY DIFFRACTIONr_sphericity_free30.52533
X-RAY DIFFRACTIONr_sphericity_bonded12.96852236
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 48 -
Rwork0.391 1151 -
obs--100 %

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