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- PDB-6avj: Crystal structure of human Mitochondrial inner NEET protein (MiNT... -

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Basic information

Entry
Database: PDB / ID: 6avj
TitleCrystal structure of human Mitochondrial inner NEET protein (MiNT)/CISD3
ComponentsCDGSH iron-sulfur domain-containing protein 3, mitochondrial
KeywordsMETAL BINDING PROTEIN / NEET-fold / Iron-Sulfur cluster / Mitochondria
Function / homology
Function and homology information


protein maturation by [2Fe-2S] cluster transfer / 2 iron, 2 sulfur cluster binding / mitochondrion / metal ion binding
Similarity search - Function
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 / CDGSH iron-sulfur domain-containing protein 3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLipper, C.H. / Karmi, O. / Sohn, Y.S. / Darash-Yahana, M. / Lammert, H. / Song, L. / Liu, A. / Mittler, R. / Nechushtai, R. / Onuchic, J.N. / Jennings, P.A.
Funding support United States, Israel, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101467 United States
National Science Foundation (NSF, United States)PHY-1427654 United States
National Science Foundation (NSF, United States)CHE-1614101 United States
Israel Science FoundationISF-865/13 Israel
National Science Foundation (NSF, United States)MCB-1613462 United States
United States - Israel Binational Science Foundation (BSF)2015831 Israel
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of the human monomeric NEET protein MiNT and its role in regulating iron and reactive oxygen species in cancer cells.
Authors: Lipper, C.H. / Karmi, O. / Sohn, Y.S. / Darash-Yahana, M. / Lammert, H. / Song, L. / Liu, A. / Mittler, R. / Nechushtai, R. / Onuchic, J.N. / Jennings, P.A.
History
DepositionSep 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CDGSH iron-sulfur domain-containing protein 3, mitochondrial
B: CDGSH iron-sulfur domain-containing protein 3, mitochondrial
C: CDGSH iron-sulfur domain-containing protein 3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7099
Polymers30,6543
Non-polymers1,0556
Water4,270237
1
A: CDGSH iron-sulfur domain-containing protein 3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5703
Polymers10,2181
Non-polymers3522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CDGSH iron-sulfur domain-containing protein 3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5703
Polymers10,2181
Non-polymers3522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CDGSH iron-sulfur domain-containing protein 3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5703
Polymers10,2181
Non-polymers3522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.406, 52.250, 78.951
Angle α, β, γ (deg.)90.000, 108.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-392-

HOH

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Components

#1: Protein CDGSH iron-sulfur domain-containing protein 3, mitochondrial / MitoNEET-related protein 2 / Miner2


Mass: 10218.052 Da / Num. of mol.: 3 / Mutation: H75C H113C
Source method: isolated from a genetically manipulated source
Details: MiNT residues 36-127 / Source: (gene. exp.) Homo sapiens (human) / Gene: CISD3 / Plasmid: pET24a / Cell line (production host): BL21-CodonPlus (DE3)-RIL / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7P0
#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM bis-tris propane, 2.5 M ammonium sulfate, 3% v/v polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 20, 2017 / Details: Varimax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→34.24 Å / Num. obs: 27910 / % possible obs: 99.36 % / Redundancy: 7.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.042 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.05 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2593 / CC1/2: 0.637 / Rpim(I) all: 0.323 / % possible all: 93.58

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å34.24 Å
Translation1.9 Å34.24 Å

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Processing

Software
NameVersionClassification
PHENIX2.7.16model building
PHENIX2.7.16refinement
PDB_EXTRACT3.22data extraction
XPREPdata reduction
APEXdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TBN

3tbn


Resolution: 1.9→34.24 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.85
RfactorNum. reflection% reflection
Rfree0.1977 2002 7.18 %
Rwork0.1689 --
obs0.171 27888 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.31 Å2 / Biso mean: 25.0375 Å2 / Biso min: 6.75 Å2
Refinement stepCycle: final / Resolution: 1.9→34.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 24 237 2391
Biso mean--14.43 31.56 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142196
X-RAY DIFFRACTIONf_angle_d1.7662946
X-RAY DIFFRACTIONf_chiral_restr0.067324
X-RAY DIFFRACTIONf_plane_restr0.008372
X-RAY DIFFRACTIONf_dihedral_angle_d12.2811380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8982-1.94560.25371360.22381701183791
1.9456-1.99820.2311350.196418161951100
1.9982-2.0570.22491450.182118371982100
2.057-2.12340.21231440.176218562000100
2.1234-2.19930.20581430.164518702013100
2.1993-2.28730.21441450.155918461991100
2.2873-2.39140.21121490.149318532002100
2.3914-2.51740.1871470.156218481995100
2.5174-2.67510.18131290.1518561985100
2.6751-2.88160.17941520.16118652017100
2.8816-3.17140.2161410.176318652006100
3.1714-3.62980.1711470.158718652012100
3.6298-4.57150.1681420.152418862028100
4.5715-34.24520.20951470.19531922206999

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