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- PDB-6hd9: Crystal structure of the potassium channel MtTMEM175 with rubidium -

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Basic information

Entry
Database: PDB / ID: 6hd9
TitleCrystal structure of the potassium channel MtTMEM175 with rubidium
Components
  • Nanobody,Maltose/maltodextrin-binding periplasmic protein
  • TMEM175
KeywordsTRANSPORT PROTEIN / lysosome / TMEM175 / potassium channel
Function / homology
Function and homology information


potassium ion leak channel activity / proton channel activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...potassium ion leak channel activity / proton channel activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Immunoglobulins ...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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / RUBIDIUM ION / Potassium channel Ftrac_2467 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesLama glama (llama)
Escherichia coli (E. coli)
Marivirga tractuosa DSM 4126 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBrunner, J.D. / Jakob, R.P. / Schulze, T. / Neldner, Y. / Moroni, A. / Thiel, G. / Maier, T. / Schenck, S.
Citation
Journal: 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.
#1: Journal: Biorxiv / Year: 2019
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
DepositionAug 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 15, 2020Group: Database references / Category: citation / citation_author
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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_atom_id / _atom_site.label_comp_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_ISSN ..._chem_comp.pdbx_synonyms / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: TMEM175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6865
Polymers82,7482
Non-polymers9383
Water21612
1
A: Nanobody,Maltose/maltodextrin-binding periplasmic protein
B: TMEM175
hetero molecules

A: Nanobody,Maltose/maltodextrin-binding periplasmic protein
B: TMEM175
hetero molecules

A: Nanobody,Maltose/maltodextrin-binding periplasmic protein
B: TMEM175
hetero molecules

A: Nanobody,Maltose/maltodextrin-binding periplasmic protein
B: TMEM175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,74520
Polymers330,9928
Non-polymers3,75412
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Unit cell
Length a, b, c (Å)130.480, 130.480, 132.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-502-

RB

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Components

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Antibody / Protein , 2 types, 2 molecules AB

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


Mass: 53267.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama), (gene. exp.) Escherichia coli (strain K12) (bacteria)
Plasmid: pBXNPHM3 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P0AEX9
#2: Protein TMEM175


Mass: 29480.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marivirga tractuosa DSM 4126 (bacteria)
Gene: Ftrac_2467 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: E4TN31

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Sugars , 2 types, 2 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.: 1
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.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 2 types, 13 molecules

#5: Chemical ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Rb
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.41 Å3/Da / Density % sol: 63.89 %
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
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.7948 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7948 Å / Relative weight: 1
ReflectionResolution: 3.5→46.5 Å / Num. obs: 14836 / % possible obs: 99.3 % / Redundancy: 27.7 % / Biso Wilson estimate: 102.3 Å2 / CC1/2: 1 / Rpim(I) all: 0.033 / Rrim(I) all: 0.279 / Net I/σ(I): 11.4
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 23 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1400 / CC1/2: 0.511 / Rpim(I) all: 0.74 / Rrim(I) all: 3.512 / % possible all: 93.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF, 5JQH

1anf

5jqh


Resolution: 3.5→21.47 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.613
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1039 7 %RANDOM
Rwork0.289 ---
obs0.289 14836 99.5 %-
Displacement parametersBiso mean: 173.49 Å2
Baniso -1Baniso -2Baniso -3
1--17.6069 Å20 Å20 Å2
2---17.6069 Å20 Å2
3---35.2137 Å2
Refine analyzeLuzzati coordinate error obs: 0.75 Å
Refinement stepCycle: 1 / Resolution: 3.5→21.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5463 0 54 15 5532
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111198HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1720295HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2455SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1548HARMONIC5
X-RAY DIFFRACTIONt_it11198HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion14.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion751SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11422SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.78 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.296 207 7.01 %
Rwork0.2811 2744 -
all0.2821 2951 -
obs--97.88 %
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)
100.111-1.08540-3.159421.0679-0.16110.39810.39860.13690.04990.4187-0.0640.45710.11120.9119-0.4559-0.13370.9119-0.0159-0.620937.7849-58.6251-20.6303
22.22890.53-1.33112.0938-1.54542.3213-0.4704-0.7586-0.3703-0.50540.19380.3437-0.38070.6690.27660.80.09320.18110.86020.085-0.441237.3171-73.689125.9918
30-7.7517-4.799.4712-0.44695.83470.01330.2190.48250.0855-0.130.1607-0.0090.03280.11670.76860.0518-0.14880.4466-0.1315-0.284714.3241-59.206747.3177
41.5089-2.08941.09162.68922.25522.5918-0.192-0.2501-0.02310.20320.3579-0.04120.05520.9084-0.16590.4436-0.12880.04130.38190.0577-0.274711.6508-58.754771.5916
51.1982-1.11142.87340.81492.503614.84140.25110.06730.12960.1038-0.5611-0.00060.09471.41220.310.3404-0.38590.10220.6848-0.0246-0.372226.4694-61.073468.39
610.73242.8501-5.11352.9344-3.23144.94810.16910.21130.6745-0.38-0.13380.25-0.1223-0.0708-0.03530.5642-0.4559-0.14780.57770.1251-0.498536.937-52.661472.3359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|4 - A|133 }
2X-RAY DIFFRACTION2{ A|134 - A|480 }
3X-RAY DIFFRACTION3{ B|9 - B|23 }
4X-RAY DIFFRACTION4{ B|24 - B|124 }
5X-RAY DIFFRACTION5{ B|125 - B|207 }
6X-RAY DIFFRACTION6{ B|208 - B|240 }

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