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- PDB-4myh: Structure of the Glutathione bound mitochondrial ABC transporter, Atm1 -

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Basic information

Entry
Database: PDB / ID: 4myh
TitleStructure of the Glutathione bound mitochondrial ABC transporter, Atm1
ComponentsIron-sulfur clusters transporter ATM1, mitochondrial
KeywordsTRANSPORT PROTEIN / ABC transporter / Membrane transport / Mitochondrial inner membrane / GLUTATHIONE
Function / homology
Function and homology information


iron-sulfur cluster transmembrane transport / Mitochondrial ABC transporters / iron-sulfur cluster export from the mitochondrion / mitochondrial transmembrane transport / Translocases / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / mitochondrial inner membrane ...iron-sulfur cluster transmembrane transport / Mitochondrial ABC transporters / iron-sulfur cluster export from the mitochondrion / mitochondrial transmembrane transport / Translocases / iron-sulfur cluster assembly / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / mitochondrial inner membrane / intracellular iron ion homeostasis / ATP hydrolysis activity / mitochondrion / ATP binding
Similarity search - Function
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Iron-sulfur clusters transporter ATM1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.38 Å
AuthorsSrinivasan, V.
CitationJournal: Science / Year: 2014
Title: Crystal structures of nucleotide-free and glutathione-bound mitochondrial ABC transporter Atm1.
Authors: Srinivasan, V. / Pierik, A.J. / Lill, R.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-sulfur clusters transporter ATM1, mitochondrial
C: Iron-sulfur clusters transporter ATM1, mitochondrial
B: Iron-sulfur clusters transporter ATM1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,9454
Polymers201,6383
Non-polymers3071
Water0
1
A: Iron-sulfur clusters transporter ATM1, mitochondrial
B: Iron-sulfur clusters transporter ATM1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,7323
Polymers134,4252
Non-polymers3071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint-115 kcal/mol
Surface area54890 Å2
MethodPISA
2
C: Iron-sulfur clusters transporter ATM1, mitochondrial

C: Iron-sulfur clusters transporter ATM1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)134,4252
Polymers134,4252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area13700 Å2
ΔGint-109 kcal/mol
Surface area53980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.686, 157.686, 523.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Iron-sulfur clusters transporter ATM1, mitochondrial


Mass: 67212.547 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 98-690
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ATM1, MDY, YMR301C, YM9952.03C / Production host: Escherichia coli (E. coli) / References: UniProt: P40416, xenobiotic-transporting ATPase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S

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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: 4.66 Å3/Da / Density % sol: 73.59 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 35% (w/v) PEE (pentaerythritol ethoxylate), 100mM MES, pH 6.5, 200mM ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.38→58.993 Å / Num. obs: 54949 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.38→3.4387 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
SHELXCDphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.38→58.993 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2899 2782 5.08 %
Rwork0.2473 --
obs0.2496 54808 99.7 %
all-54807 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.38→58.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14028 0 20 0 14048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114308
X-RAY DIFFRACTIONf_angle_d1.33419377
X-RAY DIFFRACTIONf_dihedral_angle_d16.4215231
X-RAY DIFFRACTIONf_chiral_restr0.0742262
X-RAY DIFFRACTIONf_plane_restr0.0072458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.38-3.43870.36431310.32732468X-RAY DIFFRACTION96
3.4387-3.50130.35121330.31562569X-RAY DIFFRACTION100
3.5013-3.56860.33911270.30532538X-RAY DIFFRACTION100
3.5686-3.64140.28371340.28822562X-RAY DIFFRACTION100
3.6414-3.72060.3271300.28352539X-RAY DIFFRACTION100
3.7206-3.80710.34041490.27772558X-RAY DIFFRACTION100
3.8071-3.90230.30691390.26662579X-RAY DIFFRACTION100
3.9023-4.00780.31471510.26612534X-RAY DIFFRACTION100
4.0078-4.12570.26321290.25462575X-RAY DIFFRACTION100
4.1257-4.25880.31741500.23792577X-RAY DIFFRACTION100
4.2588-4.4110.25381200.222589X-RAY DIFFRACTION100
4.411-4.58760.24851320.21412583X-RAY DIFFRACTION100
4.5876-4.79630.25621310.2072623X-RAY DIFFRACTION100
4.7963-5.0490.2551460.20752583X-RAY DIFFRACTION100
5.049-5.36510.23321590.21732593X-RAY DIFFRACTION100
5.3651-5.77910.28451360.23482632X-RAY DIFFRACTION100
5.7791-6.360.32331350.25152650X-RAY DIFFRACTION100
6.36-7.27890.25861410.25272671X-RAY DIFFRACTION100
7.2789-9.16510.24441430.1942726X-RAY DIFFRACTION100
9.1651-59.00190.33091660.26922877X-RAY DIFFRACTION99

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