[English] 日本語
Yorodumi
- EMDB-35089: Mouse Pendrin bound chloride in inward state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35089
TitleMouse Pendrin bound chloride in inward state
Map data
Sample
  • Complex: mouse Pendrin bound chloride in inward state
    • Protein or peptide: Pendrin
  • Ligand: CHLORIDE ION
Keywordsexchange / transport / slc / TRANSPORT PROTEIN
Function / homology
Function and homology information


Multifunctional anion exchangers / iodide transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / regulation of pH / chloride:bicarbonate antiporter activity / animal organ morphogenesis / brush border membrane / regulation of protein localization / apical plasma membrane ...Multifunctional anion exchangers / iodide transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / regulation of pH / chloride:bicarbonate antiporter activity / animal organ morphogenesis / brush border membrane / regulation of protein localization / apical plasma membrane / extracellular exosome / membrane
Similarity search - Function
Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsLiu QY / Zhang X / Sun L / Chen ZG
Funding support1 items
OrganizationGrant numberCountry
Not funded81900729
CitationJournal: To Be Published
Title: Mouse Pendrin bound chloride in inward state
Authors: Liu QY / Zhang X / Sun L / Chen ZG
History
DepositionJan 9, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35089.png

Downloads & links

-
Map

FileDownload / File: emd_35089.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.72 Å		1.05 Å/pix.
x 320 pix.
= 334.72 Å		1.05 Å/pix.
x 320 pix.
= 334.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.046 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.004329605 - 1.6057756
Average (Standard dev.)0.0006531808 (±0.017737588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_35089_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35089_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : mouse Pendrin bound chloride in inward state

EntireName: mouse Pendrin bound chloride in inward state
Components
  • Complex: mouse Pendrin bound chloride in inward state
    • Protein or peptide: Pendrin
  • Ligand: CHLORIDE ION

-
Supramolecule #1: mouse Pendrin bound chloride in inward state

SupramoleculeName: mouse Pendrin bound chloride in inward state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Pendrin

MacromoleculeName: Pendrin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 85.769578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAARGGRSEP PQLAEYSCSY TVSRPVYSEL AFQQQRERRL PERRTLRDSL ARSCSCSRKR AFGVVKTLLP ILDWLPKYRV KEWLLSDII SGVSTGLVGT LQGMAYALLA AVPVQFGLYS AFFPILTYFV FGTSRHISVG PFPVVSLMVG SVVLSMAPDD H FLVPSGNG ...String:
MAARGGRSEP PQLAEYSCSY TVSRPVYSEL AFQQQRERRL PERRTLRDSL ARSCSCSRKR AFGVVKTLLP ILDWLPKYRV KEWLLSDII SGVSTGLVGT LQGMAYALLA AVPVQFGLYS AFFPILTYFV FGTSRHISVG PFPVVSLMVG SVVLSMAPDD H FLVPSGNG SALNSTTLDT GTRDAARVLL ASTLTLLVGI IQLVFGGLQI GFIVRYLADP LVGGFTTAAA FQVLVSQLKI VL NVSTKNY NGILSIIYTL IEIFQNIGDT NIADFIAGLL TIIVCMAVKE LNDRFKHRIP VPIPIEVIVT IIATAISYGA NLE KNYNAG IVKSIPSGFL PPVLPSVGLF SDMLAASFSI AVVAYAIAVS VGKVYATKHD YVIDGNQEFI AFGISNVFSG FFSC FVATT ALSRTAVQES TGGKTQVAGL ISAVIVMVAI VALGRLLEPL QKSVLAAVVI ANLKGMFMQV CDVPRLWKQN KTDAV IWVF TCIMSIILGL DLGLLAGLLF ALLTVVLRVQ FPSWNGLGSV PSTDIYKSIT HYKNLEEPEG VKILRFSSPI FYGNVD GFK KCINSTVGFD AIRVYNKRLK ALRRIQKLIK KGQLRATKNG IISDIGSSNN AFEPDEDVEE PEELNIPTKE IEIQVDW NS ELPVKVNVPK VPIHSLVLDC GAVSFLDVVG VRSLRMIVKE FQRIDVNVYF ALLQDDVLEK MEQCGFFDDN IRKDRFFL T VHDAILHLQN QVKSREGQDS LLETVARIRD CKDPLDLMEA EMNAEELDVQ DEAMRRLAS

UniProtKB: Pendrin

-
Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120887
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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