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- PDB-6gci: Structure of the bongkrekic acid-inhibited mitochondrial ADP/ATP ... -

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Basic information

Entry
Database: PDB / ID: 6gci
TitleStructure of the bongkrekic acid-inhibited mitochondrial ADP/ATP carrier
Components
  • Nanobody
  • mitochondrial ADP/ATP carrier
KeywordsMEMBRANE PROTEIN / Transporter / Inhibitor / Mitochondrial / Carrier
Function / homology
Function and homology information


mitochondrial ADP transmembrane transport / ATP:ADP antiporter activity / mitochondrial ATP transmembrane transport / mitochondrial inner membrane
Similarity search - Function
ADP/ATP carrier protein, eukaryotic type / Mitochondrial carrier protein / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile.
Similarity search - Domain/homology
Bongkrekic acid / CARDIOLIPIN / ADP/ATP translocase
Similarity search - Component
Biological speciesThermothelomyces thermophila
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsRuprecht, J.J. / King, M.S. / Pardon, E. / Aleksandrova, A.A. / Zogg, T. / Crichton, P.G. / Steyaert, J. / Kunji, E.R.S.
Funding support United Kingdom, Belgium, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UU_00015/1 United Kingdom
European UnionInstruct-ERIC/ESFRI Belgium
Other governmentResearch Foundation - Flanders (FWO) Belgium
CitationJournal: Cell / Year: 2019
Title: The Molecular Mechanism of Transport by the Mitochondrial ADP/ATP Carrier.
Authors: Ruprecht, J.J. / King, M.S. / Zogg, T. / Aleksandrova, A.A. / Pardon, E. / Crichton, P.G. / Steyaert, J. / Kunji, E.R.S.
History
DepositionApr 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mitochondrial ADP/ATP carrier
B: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6549
Polymers48,5642
Non-polymers8,0897
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-17 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.650, 75.650, 295.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-301-

P6G

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Components

#1: Protein mitochondrial ADP/ATP carrier


Mass: 34042.578 Da / Num. of mol.: 1 / Mutation: Q302K
Source method: isolated from a genetically manipulated source
Details: Sequence has Q302K mutation
Source: (gene. exp.) Thermothelomyces thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus)
Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2316753 / Plasmid: pYES3 / Details (production host): modified / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): WB12 / References: UniProt: G2QNH0
#2: Antibody Nanobody


Mass: 14521.907 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Nanobody selected against the BKA-inhibited ADP/ATP carrier
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMESy4 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Chemical ChemComp-BKC / Bongkrekic acid / Bongkrek acid


Mass: 486.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H38O7
#4: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
Has protein modificationY

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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: 5.03 Å3/Da / Density % sol: 75.53 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES pH 6.5, 1% 3-methyl-3-pentanol, 22% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.3→29.35 Å / Num. obs: 13204 / % possible obs: 85.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 111.32 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.1
Reflection shellResolution: 3.3→3.43 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 659 / % possible all: 40.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IMK, 4C9H

5imk

4c9h


Resolution: 3.3→29.35 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.484 / SU Rfree Cruickshank DPI: 0.487
Details: (A) Crystal diffracted anisotropically, and data was treated with STARANISO. (B) Fourier map coefficients have been deposited along with the observed data. (C) A PEG molecule lies on a ...Details: (A) Crystal diffracted anisotropically, and data was treated with STARANISO. (B) Fourier map coefficients have been deposited along with the observed data. (C) A PEG molecule lies on a symmetry axis (special position) and has been modelled with occupancy=0.5. (D) Some cardiolipins molecules have been modelled with partial occupancy, as described in the accompanying paper. (E) Met250-Ser252 and Lys257 lie in very weak electron density. Their position is supported by good electron density obtained from an earlier crystal. (F) There are unmodelled bits of electron density near the N-terminus of the carrier, which are likely to be lipid headgroups/tails. (G) Additional electron density at the C-terminus of the carrier indicates where the C-terminal tail is likely to run, but it is not possible to model this accurately. (H) The structure factor file contains a second data block containing the structure factors from a crystal of BKA-inhibited TtAac grown without the nanobody. This P212121 crystal diffracted to lower resolution and with significant anisotropy, but was used to confirm the domain positions observed in the P3221 crystal of the TtAac-Nb complex. Full details can be found in the primary citation.
RfactorNum. reflection% reflectionSelection details
Rfree0.283 628 4.76 %RANDOM
Rwork0.252 ---
obs0.253 13203 85.1 %-
Displacement parametersBiso mean: 111.34 Å2
Baniso -1Baniso -2Baniso -3
1-3.2107 Å20 Å20 Å2
2--3.2107 Å20 Å2
3----6.4213 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: 1 / Resolution: 3.3→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 182 0 3246
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083303HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.874454HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1501SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes561HARMONIC5
X-RAY DIFFRACTIONt_it3303HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion2.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion414SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance19HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3898SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.57 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3013 -4.88 %
Rwork0.2502 1326 -
all0.2526 1394 -
obs--44.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.26051.995-0.06313.84140.27824.5032-0.17760.12510.0523-0.11590.0112-0.0320.2613-0.05220.16640.0992-0.1450.11790.1339-0.09740.0745-20.600529.8784-8.8988
26.65191.8189-2.85375.66222.38716.07780.3457-0.02880.5294-0.0425-0.2184-0.3114-0.13382.1173-0.1273-0.7065-0.28160.05-0.01370.2533-0.947-5.15734.9255-50.1961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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