[English] 日本語
Yorodumi
- EMDB-30058: KCC3 bound with DIOA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30058
TitleKCC3 bound with DIOA
Map datacryo_EM map of KCC3 bound with DIOA
Sample
  • Complex: KCC3 bound with DIOA
    • Protein or peptide: Solute carrier family 12 member 6
  • Ligand: POTASSIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid
  • Ligand: water
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) / potassium ion transmembrane transporter activity / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / cellular hypotonic response / cellular hypotonic salinity 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 ion transmembrane transporter activity / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / cellular hypotonic response / cellular hypotonic salinity response / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / monoatomic ion transport / chloride transmembrane transport / potassium ion transmembrane transport / cellular response to glucose stimulus / basolateral plasma membrane / chemical synaptic transmission / angiogenesis / 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: 2.7 Å
AuthorsChi XM / Li XR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
National Natural Science Foundation of China (NSFC)81920108015 China
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Cell Res / Year: 2021
Title: Cryo-EM structures of the full-length human KCC2 and KCC3 cation-chloride cotransporters.
Authors: Ximin Chi / Xiaorong Li / Yun Chen / Yuanyuan Zhang / Qiang Su / Qiang Zhou /
History
DepositionFeb 26, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6m22
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30058.png

Downloads & links

-
Map

FileDownload / File: emd_30058.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo_EM map of KCC3 bound with DIOA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 347.84 Å		1.09 Å/pix.
x 320 pix.
= 347.84 Å		1.09 Å/pix.
x 320 pix.
= 347.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.025
Minimum - Maximum-0.06867914 - 0.16116068
Average (Standard dev.)0.0000751686 (±0.003172606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 347.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z347.840347.840347.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0690.1610.000

-
Supplemental data

-
Sample components

-
Entire : KCC3 bound with DIOA

EntireName: KCC3 bound with DIOA
Components
  • Complex: KCC3 bound with DIOA
    • Protein or peptide: Solute carrier family 12 member 6
  • Ligand: POTASSIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid
  • Ligand: water

-
Supramolecule #1: KCC3 bound with DIOA

SupramoleculeName: KCC3 bound with DIOA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Solute carrier family 12 member 6

MacromoleculeName: Solute carrier family 12 member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 123.717906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGRMPHFTVT KVEDPEEGAA ASISQEPSLA DIKARIQDSD EPDLSQNSIT GEHSQLLDDG HKKARNAYLN NSNYEEGDE YFDKNLALFE EEMDTRPKVS SLLNRMANYT NLTQGAKEHE EAENITEGKK KPTKTPQMGT FMGVYLPCLQ N IFGVILFL ...String:
MADYKDDDDK SGRMPHFTVT KVEDPEEGAA ASISQEPSLA DIKARIQDSD EPDLSQNSIT GEHSQLLDDG HKKARNAYLN NSNYEEGDE YFDKNLALFE EEMDTRPKVS SLLNRMANYT NLTQGAKEHE EAENITEGKK KPTKTPQMGT FMGVYLPCLQ N IFGVILFL RLTWVVGTAG VLQAFAIVLI CCCCTMLTAI SMSAIATNGV VPAGGSYFMI SRALGPEFGG AVGLCFYLGT TF AAAMYIL GAIEIFLVYI VPRAAIFHSD DALKESAAML NNMRVYGTAF LVLMVLVVFI GVRYVNKFAS LFLACVIVSI LAI YAGAIK SSFAPPHFPV CMLGNRTLSS RHIDVCSKTK EINNMTVPSK LWGFFCNSSQ FFNATCDEYF VHNNVTSIQG IPGL ASGII TENLWSNYLP KGEIIEKPSA KSSDVLGSLN HEYVLVDITT SFTLLVGIFF PSVTGIMAGS NRSGDLKDAQ KSIPI GTIL AILTTSFVYL SNVVLFGACI EGVVLRDKFG DAVKGNLVVG TLSWPSPWVI VIGSFFSTCG AGLQSLTGAP RLLQAI AKD NIIPFLRVFG HSKANGEPTW ALLLTAAIAE LGILIASLDL VAPILSMFFL MCYLFVNLAC ALQTLLRTPN WRPRFRY YH WALSFMGMSI CLALMFISSW YYAIVAMVIA GMIYKYIEYQ GAEKEWGDGI RGLSLSAARF ALLRLEEGPP HTKNWRPQ L LVLLKLDEDL HVKHPRLLTF ASQLKAGKGL TIVGSVIVGN FLENYGEALA AEQTIKHLME AEKVKGFCQL VVAAKLREG ISHLIQSCGL GGMKHNTVVM GWPNGWRQSE DARAWKTFIG TVRVTTAAHL ALLVAKNISF FPSNVEQFSE GNIDVWWIVH DGGMLMLLP FLLKQHKVWR KCSIRIFTVA QLEDNSIQMK KDLATFLYHL RIEAEVEVVE MHDSDISAYT YERTLMMEQR S QMLRHMRL SKTERDREAQ LVKDRNSMLR LTSIGSDEDE ETETYQEKVH MTWTKDKYMA SRGQKAKSME GFQDLLNMRP DQ SNVRRMH TAVKLNEVIV NKSHEAKLVL LNMPGPPRNP EGDENYMEFL EVLTEGLERV LLVRGGGSEV ITIYS

UniProtKB: Solute carrier family 12 member 6

-
Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #6: 2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylid...

MacromoleculeName: 2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid
type: ligand / ID: 6 / Number of copies: 2 / Formula: EZC
Molecular weightTheoretical: 399.308 Da
Chemical component information

ChemComp-EZC:
2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid

-
Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 40 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 364959
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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