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- PDB-7yvz: Structure of Caenorhabditis elegans CISD-1/mitoNEET -

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Basic information

Entry
Database: PDB / ID: 7yvz
TitleStructure of Caenorhabditis elegans CISD-1/mitoNEET
ComponentsCDGSH iron-sulfur domain-containing protein 1 (CISD-1/mitoNEET)
KeywordsMETAL BINDING PROTEIN / Caenorhabditis elegans / mitochondrial outer membrane protein / CDGSH iron sulfur containing protein / regulating mitochondrial function and morphology
Function / homology
Function and homology information


regulation of autophagy / 2 iron, 2 sulfur cluster binding / mitochondrial outer membrane / membrane => GO:0016020 / metal ion binding
Similarity search - Function
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 / ZnF_CDGSH domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHasegawa, K. / Hagiuda, E. / Taguchi, A.T. / Geldenhuys, W. / Iwasaki, T. / Kumasaka, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24659202 Japan
Japan Society for the Promotion of Science (JSPS)26670215 Japan
Japan Society for the Promotion of Science (JSPS)2604415 Japan
Other private
CitationJournal: Adv Redox Res / Year: 2022
Title: Structure and biological evaluation of Caenorhabditis elegans CISD-1/mitoNEET, a KLP-17 tail domain homologue, supports attenuation of paraquat-induced oxidative stress through a p38 MAPK- ...Title: Structure and biological evaluation of Caenorhabditis elegans CISD-1/mitoNEET, a KLP-17 tail domain homologue, supports attenuation of paraquat-induced oxidative stress through a p38 MAPK-mediated antioxidant defense response.
Authors: Boos, J.R. / Jandrain, H.N. / Hagiuda, E. / Taguchi, A.T. / Hasegawa, K. / Fedun, B.L. / Taylor, S.J. / Elad, S.M. / Faber, S.E. / Kumasaka, T. / Iwasaki, T. / Geldenhuys, W.J.
History
DepositionAug 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title

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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 (CISD-1/mitoNEET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8072
Polymers9,6311
Non-polymers1761
Water34219
1
A: CDGSH iron-sulfur domain-containing protein 1 (CISD-1/mitoNEET)
hetero molecules

A: CDGSH iron-sulfur domain-containing protein 1 (CISD-1/mitoNEET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6144
Polymers19,2622
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3770 Å2
ΔGint-48 kcal/mol
Surface area6350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.798, 37.798, 82.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein CDGSH iron-sulfur domain-containing protein 1 (CISD-1/mitoNEET)


Mass: 9630.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A7LPG5
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 1.53 Å3/Da / Density % sol: 19.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM CHES-NaOH, pH 9.5, and 30%(w/v) PEG 3000 to which 5%(v/v) of 1 M Bicine, pH8.5, was added

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→34.35 Å / Num. obs: 7076 / % possible obs: 99.77 % / Redundancy: 7.1 % / Biso Wilson estimate: 25.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04914 / Rpim(I) all: 0.01976 / Rrim(I) all: 0.05317 / Net I/σ(I): 19.83
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 686 / CC1/2: 0.907 / CC star: 0.975 / Rpim(I) all: 0.1846 / Rrim(I) all: 0.5081

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Processing

Software
NameVersionClassification
BSSdata collection
XDSdata reduction
PHASERphasing
Cootmodel building
PHENIX1.1192.2_4158refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: rat mitoNEET

Resolution: 1.7→34.35 Å / SU ML: 0.1394 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.2787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1891 708 10.01 %
Rwork0.1677 6368 -
obs0.1699 7076 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms481 0 4 19 504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145502
X-RAY DIFFRACTIONf_angle_d1.4611678
X-RAY DIFFRACTIONf_chiral_restr0.085172
X-RAY DIFFRACTIONf_plane_restr0.011987
X-RAY DIFFRACTIONf_dihedral_angle_d5.944372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.21131370.17271236X-RAY DIFFRACTION99.71
1.83-2.010.20851390.16011247X-RAY DIFFRACTION100
2.01-2.30.19751390.15931247X-RAY DIFFRACTION99.93
2.31-2.90.20751420.18951282X-RAY DIFFRACTION99.93
2.9-34.350.17561510.16181356X-RAY DIFFRACTION99.14
Refinement TLS params.Method: refined / Origin x: 1.59145465116 Å / Origin y: 8.23809547912 Å / Origin z: 2.00553986306 Å
111213212223313233
T0.249058444563 Å20.00396857733733 Å2-0.0115413063593 Å2-0.243414989422 Å20.00739979007934 Å2--0.230692052002 Å2
L1.62107497485 °2-0.677769868925 °20.419843770301 °2-1.62227099655 °2-0.293625097474 °2--1.39537286817 °2
S0.00393875465021 Å °-0.138657401414 Å °0.156434019579 Å °0.108547820785 Å °0.0293330544022 Å °0.0561103933241 Å °-0.114688466891 Å °-0.245652336894 Å °0.000145434771175 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 38 through 100)

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