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- PDB-6paq: Structure of a bacterial Atm1-family ABC exporter with ATP bound -

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Basic information

Entry
Database: PDB / ID: 6paq
TitleStructure of a bacterial Atm1-family ABC exporter with ATP bound
ComponentsATM1-type heavy metal exporter
KeywordsTRANSPORT PROTEIN / ABC transporter / ABC exporter / ATPase / membrane protein
Function / homology
Function and homology information


Translocases / response to mercury ion / ABC-type transporter activity / monoatomic ion transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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. ...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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ATM1-type heavy metal exporter
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å
AuthorsFan, C. / Kaiser, J.T. / Rees, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: A structural framework for unidirectional transport by a bacterial ABC exporter.
Authors: Chengcheng Fan / Jens T Kaiser / Douglas C Rees /
Abstract: The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from (Atm1) can export glutathione derivatives and confer ...The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from (Atm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying the Atm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As Atm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport by Atm1. One of the disulfide crosslinked Atm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.
History
DepositionJun 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATM1-type heavy metal exporter
B: ATM1-type heavy metal exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,7754
Polymers136,7612
Non-polymers1,0142
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15670 Å2
ΔGint-57 kcal/mol
Surface area49450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.346, 115.354, 184.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 33 through 49 or resid 51...
21(chain B and (resid 33 through 49 or resid 51...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 33 through 49 or resid 51...A33 - 49
121(chain A and (resid 33 through 49 or resid 51...A51 - 59
131(chain A and (resid 33 through 49 or resid 51...A63 - 69
141(chain A and (resid 33 through 49 or resid 51...A73 - 204
151(chain A and (resid 33 through 49 or resid 51...A206 - 214
161(chain A and (resid 33 through 49 or resid 51...A216 - 294
171(chain A and (resid 33 through 49 or resid 51...A299 - 316
181(chain A and (resid 33 through 49 or resid 51...A318 - 331
191(chain A and (resid 33 through 49 or resid 51...A333 - 3458
1101(chain A and (resid 33 through 49 or resid 51...A460 - 598
1111(chain A and (resid 33 through 49 or resid 51...A701598
1121(chain A and (resid 33 through 49 or resid 51...A701
211(chain B and (resid 33 through 49 or resid 51...B33 - 49
221(chain B and (resid 33 through 49 or resid 51...B51 - 59
231(chain B and (resid 33 through 49 or resid 51...B63 - 69
241(chain B and (resid 33 through 49 or resid 51...B73 - 204
251(chain B and (resid 33 through 49 or resid 51...B33 - 701
261(chain B and (resid 33 through 49 or resid 51...B33 - 701
271(chain B and (resid 33 through 49 or resid 51...B216 - 294
281(chain B and (resid 33 through 49 or resid 51...B33 - 701
291(chain B and (resid 33 through 49 or resid 51...B33 - 701
2101(chain B and (resid 33 through 49 or resid 51...B460 - 598
2111(chain B and (resid 33 through 49 or resid 51...B701

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Components

#1: Protein ATM1-type heavy metal exporter / ATP-binding cassette transporter Atm1 / NaAtm1


Mass: 68380.250 Da / Num. of mol.: 2 / Mutation: E523Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199) (bacteria)
Strain: ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199
Gene: atm1, Saro_2631 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G506
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestN

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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: 3.51 Å3/Da / Density % sol: 64.94 % / Description: rods
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: NaCl, Tris, PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2018
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.3→38.63 Å / Num. obs: 29277 / % possible obs: 99.32 % / Redundancy: 13.2 % / Biso Wilson estimate: 103.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.054 / Rrim(I) all: 0.2 / Net I/σ(I): 11.11
Reflection shellResolution: 3.3→3.419 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.68 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 2861 / CC1/2: 0.7 / Rpim(I) all: 0.748 / Rrim(I) all: 2.784 / % possible all: 98.72

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
REFMACrefinement
PHASERphasing
AutoSolphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PAN

6pan


Resolution: 3.301→38.626 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.97
RfactorNum. reflection% reflection
Rfree0.2899 1435 4.92 %
Rwork0.2346 --
obs0.2374 29182 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 317.76 Å2 / Biso mean: 132.286 Å2 / Biso min: 36.9 Å2
Refinement stepCycle: final / Resolution: 3.301→38.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8780 0 62 0 8842
Biso mean--163.57 --
Num. residues----1134
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4865X-RAY DIFFRACTION12.359TORSIONAL
12B4865X-RAY DIFFRACTION12.359TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3006-3.41850.42551280.33372706283498
3.4185-3.55530.35981340.25292728286299
3.5553-3.7170.31811510.21612726287799
3.717-3.91280.30311470.21042726287399
3.9128-4.15770.27131480.181427572905100
4.1577-4.47820.23121500.1627712921100
4.4782-4.92810.24021310.153127702901100
4.9281-5.63930.24351490.16972778292799
5.6393-7.09770.3151520.252628222974100
7.0977-38.62820.30371450.30372963310899

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