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- PDB-6de9: mitoNEET bound to furosemide -

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Basic information

Entry
Database: PDB / ID: 6de9
TitlemitoNEET bound to furosemide
ComponentsCDGSH iron-sulfur domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / mitoNEET / FES / furosemide
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
FE2/S2 (INORGANIC) CLUSTER / Chem-FUN / CDGSH iron-sulfur domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRobart, A.R. / Geldenhuys, W.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS) United States
CitationJournal: Commun Chem / Year: 2019
Title: Crystal structure of the mitochondrial protein mitoNEET bound to a benze-sulfonide ligand.
Authors: Geldenhuys, W.J. / Long, T.E. / Saralkar, P. / Iwasaki, T. / Nunez, R.A.A. / Nair, R.R. / Konkle, M.E. / Menze, M.A. / Pinti, M.V. / Hollander, J.M. / Hazlehurst, L.A. / Robart, A.R.
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6853
Polymers9,1791
Non-polymers5072
Water84747
1
A: CDGSH iron-sulfur domain-containing protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)19,3706
Polymers18,3572
Non-polymers1,0134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area4860 Å2
ΔGint-57 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.830, 58.830, 176.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

21A-345-

HOH

31A-347-

HOH

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Components

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


Mass: 9178.610 Da / Num. of mol.: 1 / Fragment: UNP residues 32-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CISD1, C10orf70, ZCD1, MDS029 / Plasmid: pET11a-His-SUMO-mitoNEET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NZ45
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-FUN / 5-(AMINOSULFONYL)-4-CHLORO-2-[(2-FURYLMETHYL)AMINO]BENZOIC ACID / Furosemide


Mass: 330.744 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11ClN2O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4.34 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% v/v Tacsimate TM, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.74 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2018
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 1.95→30.3 Å / Num. obs: 11815 / % possible obs: 99.92 % / Redundancy: 21.8 % / Biso Wilson estimate: 38.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0353 / Rpim(I) all: 0.021 / Rrim(I) all: 0.1 / Net I/σ(I): 40.9 / Num. measured all: 257706 / Scaling rejects: 840
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-2.0221.10.25332.247990.7960.2981.378100
8.94-30.321.70.0661590.9990.0130.06898.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3REE

3ree


Resolution: 1.95→30.3 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.31
RfactorNum. reflection% reflection
Rfree0.221 1180 10.01 %
Rwork0.1997 --
obs0.2016 11791 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.51 Å2 / Biso mean: 42.3479 Å2 / Biso min: 25.06 Å2
Refinement stepCycle: final / Resolution: 1.95→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms617 0 25 47 689
Biso mean--93.3 41.46 -
Num. residues----75
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.95-2.020.32731440.31711296
2.02-2.14640.26181420.25921283
2.1464-2.28090.27211450.22971297
2.2809-2.45690.28581470.21961321
2.4569-2.7040.21861440.2131300
2.704-3.0950.27651480.23121331
3.095-3.8980.20521500.17921347
3.898-30.30.17671600.16951436

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