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- PDB-6hdb: Crystal structure of the potassium channel MtTMEM175 with zinc -

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Basic information

Entry
Database: PDB / ID: 6hdb
TitleCrystal structure of the potassium channel MtTMEM175 with zinc
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 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 DSM 4126 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 4, 2019Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.2Sep 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 1.3Apr 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

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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)83,7447
Polymers82,7482
Non-polymers9975
Water34219
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)334,97828
Polymers330,9928
Non-polymers3,98620
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)131.920, 131.920, 132.790
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-

K

21B-503-

K

31B-504-

ZN

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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 / Plasmid: pBXC3H / 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 , 3 types, 22 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 3.49 Å3/Da / Density % sol: 64.77 %
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: 1.2461 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: 1.2461 Å / Relative weight: 1
ReflectionResolution: 2.9→46.64 Å / Num. obs: 26575 / % possible obs: 99.9 % / Redundancy: 27 % / Biso Wilson estimate: 125.03 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Rrim(I) all: 0.177 / Net I/σ(I): 10.2
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 27.1 % / Num. unique obs: 2588 / Rpim(I) all: 2.23 / Rrim(I) all: 14.32 / % possible all: 99.8

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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: 2.9→44.1 Å / Cor.coef. Fo:Fc: 0.801 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.881 / SU Rfree Blow DPI: 0.372
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2126 8 %RANDOM
Rwork0.275 ---
obs0.276 26575 99.9 %-
Displacement parametersBiso mean: 162.04 Å2
Baniso -1Baniso -2Baniso -3
1--19.47 Å20 Å20 Å2
2---19.47 Å20 Å2
3---38.94 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: 1 / Resolution: 2.9→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5463 0 56 29 5548
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811198HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9220295HARMONIC2
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_torsion2.55
X-RAY DIFFRACTIONt_other_torsion15.94
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_contact11569SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.02 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3284 234 7.98 %
Rwork0.2764 2697 -
all0.2807 2931 -
obs--99.35 %
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)
10-0.67330.80360-3.061116.8697-0.08730.06450.15190.419-0.0072-0.0190.08661.00850.09450.4858-0.4086-0.14130.4885-0.0323-0.485638.0353-59.2341-20.5697
24.4558-0.1276-1.22765.9694-1.87065.0558-0.2824-0.2476-0.6314-0.5075-0.0747-0.08890.07420.98530.3571-0.0834-0.00120.1376-0.00250.0061-0.503137.544-74.26826.0619
30.036-8.54521.6536.05751.43162.82640.0185-0.02030.35980.0302-0.02320.1718-0.05230.03590.00470.52950.0608-0.00990.30430.0778-0.244614.4736-59.843247.3431
42.6425-2.3137-0.184.4417-0.03832.20310.1310.07350.1813-0.12070.0134-0.1208-0.97950.7028-0.1444-0.1885-0.108-0.03490.09410.0355-0.03211.7621-59.383371.6127
52.7524-0.03321.77391.79551.08679.5284-0.0109-0.07330.20930.0983-0.1026-0.1507-0.17820.76630.1136-0.0079-0.15650.03560.1885-0.0165-0.232326.5927-61.657768.435
66.99294.1193-3.79630.00273.41964.21670.0798-0.07180.2824-0.126-0.1707-0.1182-0.0930.10410.09090.2002-0.4475-0.12380.30690.0887-0.368237.028-53.210272.391
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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