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- PDB-7p0p: NAF-1 bound to M1 molecule -

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Basic information

Entry
Database: PDB / ID: 7p0p
TitleNAF-1 bound to M1 molecule
ComponentsCDGSH iron-sulfur domain-containing protein 2
KeywordsMETAL BINDING PROTEIN / [2Fe-2S] proteins / NEET proteins / destabilizer / M1
Function / homology
Function and homology information


perinuclear endoplasmic reticulum / regulation of autophagy / 2 iron, 2 sulfur cluster binding / autophagy / mitochondrial outer membrane / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / RNA binding ...perinuclear endoplasmic reticulum / regulation of autophagy / 2 iron, 2 sulfur cluster binding / autophagy / mitochondrial outer membrane / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / RNA binding / membrane / 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 / FE2/S2 (INORGANIC) CLUSTER / CDGSH iron-sulfur domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 2
B: CDGSH iron-sulfur domain-containing protein 2
C: CDGSH iron-sulfur domain-containing protein 2
D: CDGSH iron-sulfur domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3879
Polymers36,3064
Non-polymers1,0815
Water1,42379
1
A: CDGSH iron-sulfur domain-containing protein 2
B: CDGSH iron-sulfur domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5054
Polymers18,1532
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-47 kcal/mol
Surface area7210 Å2
MethodPISA
2
C: CDGSH iron-sulfur domain-containing protein 2
D: CDGSH iron-sulfur domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8825
Polymers18,1532
Non-polymers7293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-46 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.573, 47.589, 125.948
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 2 / Endoplasmic reticulum intermembrane small protein / MitoNEET-related 1 protein / Miner1 / Nutrient- ...Endoplasmic reticulum intermembrane small protein / MitoNEET-related 1 protein / Miner1 / Nutrient-deprivation autophagy factor-1 / NAF-1


Mass: 9076.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CISD2, CDGSH2, ERIS, ZCD2 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8N5K1
#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: isolated from a natural source / 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: isolated from a natural source / Formula: C22H19NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 32% PEG-3000, 100 mM Tris-HCl (pH 8.0), 100mM NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.74→47.59 Å / Num. obs: 27507 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC1/2: 0.994 / Net I/σ(I): 8.8
Reflection shellResolution: 1.74→1.77 Å / Num. unique obs: 1487 / CC1/2: 0.381

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FNV

3fnv


Resolution: 1.74→41.21 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.072 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 959 3.5 %RANDOM
Rwork0.204 ---
obs0.206 26499 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--1.04 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.74→41.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 43 79 2190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132171
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172135
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.6522895
X-RAY DIFFRACTIONr_angle_other_deg1.2651.6054935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1595259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54224.257101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94115422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.937158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02442
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_it2.5293.1011048
X-RAY DIFFRACTIONr_mcbond_other2.5183.0961047
X-RAY DIFFRACTIONr_mcangle_it3.7674.6221303
X-RAY DIFFRACTIONr_mcangle_other3.7664.6271304
X-RAY DIFFRACTIONr_scbond_it3.0083.4871123
X-RAY DIFFRACTIONr_scbond_other3.0123.4961120
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8915.0811583
X-RAY DIFFRACTIONr_long_range_B_refined6.48936.1112278
X-RAY DIFFRACTIONr_long_range_B_other6.48936.122275
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 69 -
Rwork0.338 1920 -
obs--99.9 %

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