[English] 日本語
Yorodumi
- EMDB-10703: Structure of Human Potassium Chloride Transporter KCC3 in NaCl -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10703
TitleStructure of Human Potassium Chloride Transporter KCC3 in NaCl
Map data
Sample
  • Complex: Homodimeric complex of human potassium chloride transporter
    • Protein or peptide: Solute carrier family 12 member 6
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsDimer / transporter / potassium chloride / KCC3 / SLC12A6 / membrane protein / APC / Structural Genomics / Structural Genomics Consortium / SGC / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) / potassium:chloride symporter activity / potassium ion transmembrane transporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / cellular hypotonic salinity response / cellular hypotonic response / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane ...Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) / potassium:chloride symporter activity / potassium ion transmembrane transporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / cellular hypotonic salinity response / cellular hypotonic response / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / monoatomic ion transport / potassium ion transmembrane transport / chloride transmembrane transport / cellular response to glucose stimulus / angiogenesis / chemical synaptic transmission / basolateral plasma membrane / axon / synapse / protein kinase binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
K/Cl co-transporter / SLC12A transporter, C-terminal / Solute carrier family 12 / Amino acid permease/ SLC12A domain / SLC12A transporter family / Amino acid permease
Similarity search - Domain/homology
Solute carrier family 12 member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsChi G / Man H
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
European Commission115766 United Kingdom
CitationJournal: To be published
Title: Structure of Human Potassium Chloride Transporter KCC3 in NaCl
Authors: Chi G / Man H / Ebenhoch R / Reggiano G / Pike ACW / Wang D / McKinley G / Mukhopadhyay SMM / Chalk R / Moreau C / Snee M / Bohstedt T / Singh NK / Abrusci P / Arrowsmith CH / Bountra C / ...Authors: Chi G / Man H / Ebenhoch R / Reggiano G / Pike ACW / Wang D / McKinley G / Mukhopadhyay SMM / Chalk R / Moreau C / Snee M / Bohstedt T / Singh NK / Abrusci P / Arrowsmith CH / Bountra C / Edwards AM / Marsden BD / Burgess-Brown NA / DiMaio F / Duerr KL / Structural Genomics Consortium (SGC)
History
DepositionFeb 25, 2020-
Header (metadata) releaseMar 11, 2020-
Map releaseMar 11, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6y5r
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10703.png

Downloads & links

-
Map

FileDownload / File: emd_10703.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 440 pix.
= 286.44 Å		0.65 Å/pix.
x 440 pix.
= 286.44 Å		0.65 Å/pix.
x 440 pix.
= 286.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.020708172 - 0.042289127
Average (Standard dev.)0.00006021436 (±0.0012882311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 286.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6510.6510.651
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z286.440286.440286.440
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0210.0420.000

-
Supplemental data

-
Half map: #1

Fileemd_10703_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_10703_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homodimeric complex of human potassium chloride transporter

EntireName: Homodimeric complex of human potassium chloride transporter
Components
  • Complex: Homodimeric complex of human potassium chloride transporter
    • Protein or peptide: Solute carrier family 12 member 6
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Homodimeric complex of human potassium chloride transporter

SupramoleculeName: Homodimeric complex of human potassium chloride transporter
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 246 KDa

-
Macromolecule #1: Solute carrier family 12 member 6

MacromoleculeName: Solute carrier family 12 member 6 / type: protein_or_peptide / ID: 1
Details: Sugar molecules from glycosylation post-translational modifications (NAG, BMA) present.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 122.273344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPHFTVTKVE DPEEGAAASI SQEPSLADIK ARIQDSDEPD LSQNDITGEH SQLLDDGHKK ARNAYLNNSN YEEGDEYFDK NLALFEEEM DTRPKVSSLL NRMANYTNLT QGAKEHEEAE NITEGKKKPT KTPQMGTFMG VYLPCLQNIF GVILFLRLTW V VGTAGVLQ ...String:
MPHFTVTKVE DPEEGAAASI SQEPSLADIK ARIQDSDEPD LSQNDITGEH SQLLDDGHKK ARNAYLNNSN YEEGDEYFDK NLALFEEEM DTRPKVSSLL NRMANYTNLT QGAKEHEEAE NITEGKKKPT KTPQMGTFMG VYLPCLQNIF GVILFLRLTW V VGTAGVLQ AFAIVLICCC CTMLTAISMS AIATNGVVPA GGSYFMISRA LGPEFGGAVG LCFYLGTTFA AAMYILGAIE IF LVYIVPR AAIFHSDDAL KESAAMLNNM RVYGTAFLVL MVLVVFIGVR YVNKFASLFL ACVIVSILAI YAGAIKSSFA PPH FPVCML GNRTLSSRHI DVCSKTKEIN NMTVPSKLWG FFCNSSQFFN ATCDEYFVHN NVTSIQGIPG LASGIITENL WSNY LPKGE IIEKPSAKSS DVLGSLNHEY VLVDITTSFT LLVGIFFPSV TGIMAGSNRS GDLKDAQKSI PIGTILAILT TSFVY LSNV VLFGACIEGV VLRDKFGDAV KGNLVVGTLS WPSPWVIVIG SFFSTCGAGL QSLTGAPRLL QAIAKDNIIP FLRVFG HSK ANGEPTWALL LTAAIAELGI LIASLDLVAP ILSMFFLMCY LFVNLACALQ TLLRTPNWRP RFRYYHWALS FMGMSIC LA LMFISSWYYA IVAMVIAGMI YKYIEYQGAE KEWGDGIRGL SLSAARFALL RLEEGPPHTK NWRPQLLVLL KLDEDLHV K HPRLLTFASQ LKAGKGLTIV GSVIVGNFLE NYGEALAAEQ TIKHLMEAEK VKGFCQLVVA AKLREGISHL IQSCGLGGM KHNTVVMGWP NGWRQSEDAR AWKTFIGTVR VTTAAHLALL VAKNISFFPS NVEQFSEGNI DVWWIVHDGG MLMLLPFLLK QHKVWRKCS IRIFTVAQLE DNSIQMKKDL ATFLYHLRIE AEVEVVEMHD SDISAYTYER DLMMEQRSQM LRHMRLSKTE R DREAQLVK DRNSMLRLTS IGSDEDEETE TYQEKVHMDW TKDKYMASRG QKAKSMEGFQ DLLNMRPDQS NVRRMHTAVK LN EVIVNKS HEAKLVLLNM PGPPRNPEGD ENYMEFLEVL TEGLERVLLV RGGGSEVITI YS

UniProtKB: Solute carrier family 12 member 6

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV
Details: 2 second blotting time, 40 second waiting time, -15 blotting force.
DetailsThis sample was monodisperse.

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16472 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.3000000000000003 µm / Nominal defocus min: -0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Details: map was built ab initio using Relion 3.0.8's initial model program
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 920574
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.8)
FSC plot (resolution estimation)

+
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