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- PDB-6par: Structure of a bacterial Atm1-family ABC exporter with MgAMPPNP bound -

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Basic information

Entry
Database: PDB / ID: 6par
TitleStructure of a bacterial Atm1-family ABC exporter with MgAMPPNP 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATM1-type heavy metal exporter
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 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 / Derived calculations / Category: citation / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
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

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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
C: ATM1-type heavy metal exporter
D: ATM1-type heavy metal exporter
E: ATM1-type heavy metal exporter
F: ATM1-type heavy metal exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,81318
Polymers406,6306
Non-polymers3,18312
Water00
1
A: ATM1-type heavy metal exporter
B: ATM1-type heavy metal exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,6046
Polymers135,5432
Non-polymers1,0614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16760 Å2
ΔGint-96 kcal/mol
Surface area47440 Å2
MethodPISA
2
C: ATM1-type heavy metal exporter
D: ATM1-type heavy metal exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,6046
Polymers135,5432
Non-polymers1,0614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16600 Å2
ΔGint-100 kcal/mol
Surface area48370 Å2
MethodPISA
3
E: ATM1-type heavy metal exporter
F: ATM1-type heavy metal exporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,6046
Polymers135,5432
Non-polymers1,0614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16960 Å2
ΔGint-98 kcal/mol
Surface area47760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.648, 92.498, 237.691
Angle α, β, γ (deg.)90.000, 110.340, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 38 through 53 or resid 55...
21(chain B and (resid 38 through 53 or resid 55...
31(chain C and (resid 38 through 53 or resid 55...
41(chain D and (resid 38 through 53 or resid 55...
51(chain E and (resid 38 through 53 or resid 55...
61(chain F and (resid 38 through 53 or resid 55...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 38 through 53 or resid 55...A38 - 53
121(chain A and (resid 38 through 53 or resid 55...A55 - 56
131(chain A and (resid 38 through 53 or resid 55...A62 - 68
141(chain A and (resid 38 through 53 or resid 55...A75 - 106
151(chain A and (resid 38 through 53 or resid 55...A22 - 702
161(chain A and (resid 38 through 53 or resid 55...A22 - 702
171(chain A and (resid 38 through 53 or resid 55...A124 - 144
181(chain A and (resid 38 through 53 or resid 55...A22 - 702
191(chain A and (resid 38 through 53 or resid 55...A22 - 702
1101(chain A and (resid 38 through 53 or resid 55...A323 - 333
1111(chain A and (resid 38 through 53 or resid 55...A335 - 336
1121(chain A and (resid 38 through 53 or resid 55...A3
1131(chain A and (resid 38 through 53 or resid 55...A473 - 495
1141(chain A and (resid 38 through 53 or resid 55...A497 - 540
1151(chain A and (resid 38 through 53 or resid 55...A497 - 540
1161(chain A and (resid 38 through 53 or resid 55...A542 - 569
1171(chain A and (resid 38 through 53 or resid 55...A571
1181(chain A and (resid 38 through 53 or resid 55...A573 - 598
1191(chain A and (resid 38 through 53 or resid 55...A701 - 702
211(chain B and (resid 38 through 53 or resid 55...B38 - 53
221(chain B and (resid 38 through 53 or resid 55...B55 - 56
231(chain B and (resid 38 through 53 or resid 55...B62 - 68
241(chain B and (resid 38 through 53 or resid 55...B17 - 702
251(chain B and (resid 38 through 53 or resid 55...B17 - 702
261(chain B and (resid 38 through 53 or resid 55...B17 - 702
271(chain B and (resid 38 through 53 or resid 55...B124 - 144
281(chain B and (resid 38 through 53 or resid 55...B17 - 702
291(chain B and (resid 38 through 53 or resid 55...B17 - 702
2101(chain B and (resid 38 through 53 or resid 55...B323 - 333
2111(chain B and (resid 38 through 53 or resid 55...B335 - 336
2121(chain B and (resid 38 through 53 or resid 55...B3
2131(chain B and (resid 38 through 53 or resid 55...B473 - 495
2141(chain B and (resid 38 through 53 or resid 55...B497 - 540
2151(chain B and (resid 38 through 53 or resid 55...B497 - 540
2161(chain B and (resid 38 through 53 or resid 55...B542 - 569
2171(chain B and (resid 38 through 53 or resid 55...B571
2181(chain B and (resid 38 through 53 or resid 55...B573 - 598
2191(chain B and (resid 38 through 53 or resid 55...B701 - 702
311(chain C and (resid 38 through 53 or resid 55...C38 - 53
321(chain C and (resid 38 through 53 or resid 55...C55 - 56
331(chain C and (resid 38 through 53 or resid 55...C62 - 68
341(chain C and (resid 38 through 53 or resid 55...C26 - 702
351(chain C and (resid 38 through 53 or resid 55...C26 - 702
361(chain C and (resid 38 through 53 or resid 55...C26 - 702
371(chain C and (resid 38 through 53 or resid 55...C124 - 144
381(chain C and (resid 38 through 53 or resid 55...C26 - 702
391(chain C and (resid 38 through 53 or resid 55...C26 - 702
3101(chain C and (resid 38 through 53 or resid 55...C323 - 333
3111(chain C and (resid 38 through 53 or resid 55...C335 - 336
3121(chain C and (resid 38 through 53 or resid 55...C3
3131(chain C and (resid 38 through 53 or resid 55...C473 - 495
3141(chain C and (resid 38 through 53 or resid 55...C497 - 540
3151(chain C and (resid 38 through 53 or resid 55...C497 - 540
3161(chain C and (resid 38 through 53 or resid 55...C542 - 569
3171(chain C and (resid 38 through 53 or resid 55...C571
3181(chain C and (resid 38 through 53 or resid 55...C573 - 702
411(chain D and (resid 38 through 53 or resid 55...D38 - 53
421(chain D and (resid 38 through 53 or resid 55...D55 - 56
431(chain D and (resid 38 through 53 or resid 55...D62 - 68
441(chain D and (resid 38 through 53 or resid 55...D75 - 106
451(chain D and (resid 38 through 53 or resid 55...D108 - 122
461(chain D and (resid 38 through 53 or resid 55...D124 - 144
471(chain D and (resid 38 through 53 or resid 55...D146 - 204
481(chain D and (resid 38 through 53 or resid 55...D206 - 312
491(chain D and (resid 38 through 53 or resid 55...D314 - 3121
4101(chain D and (resid 38 through 53 or resid 55...D323 - 333
4111(chain D and (resid 38 through 53 or resid 55...D335333
4121(chain D and (resid 38 through 53 or resid 55...D335 - 336
4131(chain D and (resid 38 through 53 or resid 55...D338 - 339
4141(chain D and (resid 38 through 53 or resid 55...D343
4151(chain D and (resid 38 through 53 or resid 55...D345 - 471
4161(chain D and (resid 38 through 53 or resid 55...D473 - 495
4171(chain D and (resid 38 through 53 or resid 55...D571
4181(chain D and (resid 38 through 53 or resid 55...D571
4191(chain D and (resid 38 through 53 or resid 55...D573 - 598
4201(chain D and (resid 38 through 53 or resid 55...D701 - 702
511(chain E and (resid 38 through 53 or resid 55...E38 - 53
521(chain E and (resid 38 through 53 or resid 55...E55 - 56
531(chain E and (resid 38 through 53 or resid 55...E62 - 68
541(chain E and (resid 38 through 53 or resid 55...E124 - 144
551(chain E and (resid 38 through 53 or resid 55...E34 - 702
561(chain E and (resid 38 through 53 or resid 55...E146 - 204
571(chain E and (resid 38 through 53 or resid 55...E34 - 702
581(chain E and (resid 38 through 53 or resid 55...E314 - 316
591(chain E and (resid 38 through 53 or resid 55...E34 - 702
5101(chain E and (resid 38 through 53 or resid 55...E323 - 3
5111(chain E and (resid 38 through 53 or resid 55...E343 - 38
5121(chain E and (resid 38 through 53 or resid 55...E343
5131(chain E and (resid 38 through 53 or resid 55...E345 - 471
5141(chain E and (resid 38 through 53 or resid 55...E34 - 702
5151(chain E and (resid 38 through 53 or resid 55...E542 - 569
5161(chain E and (resid 38 through 53 or resid 55...E34 - 702
5171(chain E and (resid 38 through 53 or resid 55...E571
5181(chain E and (resid 38 through 53 or resid 55...E571
5191(chain E and (resid 38 through 53 or resid 55...E573 - 702
611(chain F and (resid 38 through 53 or resid 55...F38 - 53
621(chain F and (resid 38 through 53 or resid 55...F55 - 56
631(chain F and (resid 38 through 53 or resid 55...F62 - 68
641(chain F and (resid 38 through 53 or resid 55...F22 - 702
651(chain F and (resid 38 through 53 or resid 55...F22 - 702
661(chain F and (resid 38 through 53 or resid 55...F22 - 702
671(chain F and (resid 38 through 53 or resid 55...F124 - 144
681(chain F and (resid 38 through 53 or resid 55...F22 - 702
691(chain F and (resid 38 through 53 or resid 55...F22 - 702
6101(chain F and (resid 38 through 53 or resid 55...F323 - 333
6111(chain F and (resid 38 through 53 or resid 55...F335 - 336
6121(chain F and (resid 38 through 53 or resid 55...F3
6131(chain F and (resid 38 through 53 or resid 55...F473 - 495
6141(chain F and (resid 38 through 53 or resid 55...F497 - 540
6151(chain F and (resid 38 through 53 or resid 55...F497 - 540
6161(chain F and (resid 38 through 53 or resid 55...F542 - 569
6171(chain F and (resid 38 through 53 or resid 55...F571
6181(chain F and (resid 38 through 53 or resid 55...F573 - 598
6191(chain F and (resid 38 through 53 or resid 55...F701 - 702

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Components

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


Mass: 67771.602 Da / Num. of mol.: 6
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
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: 4.3 Å3/Da / Density % sol: 71.4 % / Description: plates
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: ADA, PEG1500, PEG1000

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.97946
SYNCHROTRONSSRL BL12-220.9793
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMar 27, 2018
DECTRIS PILATUS 6M2PIXELMay 19, 2018
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Liquid nitrogen-cooled double crystal, non fixed exit slit Si(111)SINGLE WAVELENGTHMx-ray1
2Liquid nitrogen-cooled double crystal, non fixed exit slit Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.97931
Reflection

Entry-ID: 6PAR

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
3.35-39.6199850797.85791.20.9990.1740.0710.18919.43
3.6-39.857909498.17.194.990.9940.2110.0860.22827.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
3.35-3.476.41.7680.9790410.530.7541.927191.11
3.6-3.676.91.9421.143760.4660.7872.1295.8

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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: 3.35→39.619 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.01
RfactorNum. reflection% reflection
Rfree0.2816 4897 5 %
Rwork0.2538 --
obs0.2551 97915 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 356.72 Å2 / Biso mean: 120.0215 Å2 / Biso min: 13.79 Å2
Refinement stepCycle: final / Resolution: 3.35→39.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26783 0 192 0 26975
Biso mean--101.67 --
Num. residues----3452
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14693X-RAY DIFFRACTION11.717TORSIONAL
12B14693X-RAY DIFFRACTION11.717TORSIONAL
13C14693X-RAY DIFFRACTION11.717TORSIONAL
14D14693X-RAY DIFFRACTION11.717TORSIONAL
15E14693X-RAY DIFFRACTION11.717TORSIONAL
16F14693X-RAY DIFFRACTION11.717TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3501-3.38820.39741300.37572763289387
3.3882-3.4280.36381410.34612951309294
3.428-3.46980.33831540.33732896305093
3.4698-3.51370.3641380.32183118325698
3.5137-3.55990.33511370.28893174331199
3.5599-3.60860.29581640.2763045320999
3.6086-3.66010.26751720.26753122329499
3.6601-3.71470.31141770.27883153333099
3.7147-3.77270.34841740.27613062323699
3.7727-3.83450.33311470.26273143329099
3.8345-3.90060.28551360.2663123325999
3.9006-3.97150.3411740.254331363310100
3.9715-4.04780.29311750.25783137331299
4.0478-4.13030.29051850.2430923277100
4.1303-4.220.26551670.2383130329799
4.22-4.31810.28291710.2323104327599
4.3181-4.42590.25441500.223069321997
4.4259-4.54540.25651720.22222971314395
4.5454-4.6790.25481690.23223095326498
4.679-4.82980.26471790.221331783357100
4.8298-5.00210.25551850.225231053290100
5.0021-5.20190.24731500.229531703320100
5.2019-5.43810.25741770.227331753352100
5.4381-5.7240.30131790.24563120329999
5.724-6.08150.29891580.25483168332699
6.0815-6.54910.28091960.25133090328698
6.5491-7.20460.25121520.24843083323596
7.2046-8.23890.23911720.214531843356100
8.2389-10.34950.22211640.196232363400100
10.3495-39.62190.31161520.31993225337797

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