[English] 日本語
Yorodumi
- PDB-6swr: Crystal structure of the lysosomal potassium channel MtTMEM175 T3... -

+
Open data


ID or keywords:

Loading...

-
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 protein
  • 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 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 / : / 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
Revision 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
Antibody / Protein , 2 types, 4 molecules ADBE

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

-
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

-
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


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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more