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- PDB-6swr: Crystal structure of the lysosomal potassium channel MtTMEM175 T3... -

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Basic information

Entry
Database: PDB / ID: 6swr
TitleCrystal structure of the lysosomal potassium channel MtTMEM175 T38A mutant soaked with zinc
Components
  • Nanobody, Maltose/maltodextrin-binding periplasmic protein,Maltodextrin-binding protein,Maltose/maltodextrin-binding periplasmic proteinSingle-domain antibody
  • Uncharacterized protein
KeywordsTRANSPORT PROTEIN / lysosome / TMEM175 / potassium channel / Parkinson disease
Function / homology
Function and homology information


potassium ion leak channel activity / proton channel activity / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport ...potassium ion leak channel activity / proton channel activity / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / potassium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / DNA damage response / membrane / plasma membrane
Similarity search - Function
Endosomal/lysomomal potassium channel TMEM175 / Endosomal/lysosomal potassium channel TMEM175 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / : / Potassium channel Ftrac_2467 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesLama glama (llama)
Escherichia coli (E. coli)
Marivirga tractuosa
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBrunner, J.D. / Jakob, R.P. / Schulze, T. / Neldner, Y. / Moroni, A. / Thiel, G. / Maier, T. / Schenck, S.
CitationJournal: Elife / Year: 2020
Title: Structural basis for ion selectivity in TMEM175 K + channels.
Authors: Brunner, J.D. / Jakob, R.P. / Schulze, T. / Neldner, Y. / Moroni, A. / Thiel, G. / Maier, T. / Schenck, S.
History
DepositionSep 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 30, 2020Group: Database references / Structure summary / Category: chem_comp / citation / Item: _chem_comp.pdbx_synonyms / _citation.title
Revision 2.2Jan 24, 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
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: Nanobody, Maltose/maltodextrin-binding periplasmic protein,Maltodextrin-binding protein,Maltose/maltodextrin-binding periplasmic protein
B: Uncharacterized protein
D: Nanobody, Maltose/maltodextrin-binding periplasmic protein,Maltodextrin-binding protein,Maltose/maltodextrin-binding periplasmic protein
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,1819
Polymers165,4364
Non-polymers1,7455
Water55831
1
A: Nanobody, Maltose/maltodextrin-binding periplasmic protein,Maltodextrin-binding protein,Maltose/maltodextrin-binding periplasmic protein
B: Uncharacterized protein
D: Nanobody, Maltose/maltodextrin-binding periplasmic protein,Maltodextrin-binding protein,Maltose/maltodextrin-binding periplasmic protein
E: Uncharacterized protein
hetero molecules

A: Nanobody, Maltose/maltodextrin-binding periplasmic protein,Maltodextrin-binding protein,Maltose/maltodextrin-binding periplasmic protein
B: Uncharacterized protein
D: Nanobody, Maltose/maltodextrin-binding periplasmic protein,Maltodextrin-binding protein,Maltose/maltodextrin-binding periplasmic protein
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,36218
Polymers330,8728
Non-polymers3,49010
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)129.788, 131.611, 151.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Antibody / Protein , 2 types, 4 molecules ADBE

#1: Antibody Nanobody, Maltose/maltodextrin-binding periplasmic protein,Maltodextrin-binding protein,Maltose/maltodextrin-binding periplasmic protein / Single-domain antibody / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 53267.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama), (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: malE, b4034, JW3994 / Plasmid: pBXNPHM3 / Strain: K12 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P0AEX9
#2: Protein Uncharacterized protein


Mass: 29450.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marivirga tractuosa (strain ATCC 23168 / DSM 4126 / NBRC 15989 / NCIMB 1408 / VKM B-1430 / H-43) (bacteria)
Strain: ATCC 23168 / DSM 4126 / NBRC 15989 / NCIMB 1408 / VKM B-1430 / H-43
Gene: Ftrac_2467 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: E4TN31

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Sugars , 2 types, 4 molecules

#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 2 types, 32 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.24 Å3/Da / Density % sol: 70.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl pH 8.5, 150 mM NaCl, 150 mM MgCl2 and 28-30 % PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.280961 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.280961 Å / Relative weight: 1
ReflectionResolution: 3.2→49.72 Å / Num. obs: 43526 / % possible obs: 99.8 % / Redundancy: 51.8 % / Biso Wilson estimate: 76.29 Å2 / CC1/2: 0.993 / Net I/σ(I): 6.5
Reflection shellResolution: 3.2→3.32 Å / Num. unique obs: 4510 / CC1/2: 0.663

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Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF, 5JQH

1anf

5jqh


Resolution: 3.2→49.72 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.299 --
Rwork0.269 --
obs-43526 99.8 %
Refinement stepCycle: LAST / Resolution: 3.2→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10806 0 107 49 10962

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