[English] 日本語
Yorodumi
- EMDB-27267: CryoEM structures of bAE1 captured in multiple states. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27267
TitleCryoEM structures of bAE1 captured in multiple states.
Map dataMain final full map.
Sample
  • Organelle or cellular component: band 3 anion transport protein
    • Protein or peptide: Anion exchange protein
KeywordscryoEM / Band3 / bAE1 (SLC4A1) / anion exchanger / STRUCTURAL PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


monoatomic anion transmembrane transporter activity / solute:inorganic anion antiporter activity / plasma membrane
Similarity search - Function
Anion exchange protein 1 / Anion exchange protein / Anion exchange, conserved site / Anion exchangers family signature 1. / Anion exchangers family signature 2. / Band 3 cytoplasmic domain / Band 3 cytoplasmic domain / Phosphotransferase/anion transporter / Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter integral membrane domain
Similarity search - Domain/homology
Anion exchange protein
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZhekova HR / Wang WG / Jiang JS / Tsirulnikov K / Muhammad-Khan GH / Azimov R / Abuladze N / Kao L / Newman D / Noskov SY ...Zhekova HR / Wang WG / Jiang JS / Tsirulnikov K / Muhammad-Khan GH / Azimov R / Abuladze N / Kao L / Newman D / Noskov SY / Teleman P / Zhou ZH / Pushkin A / Kurtz I
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK077162 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01GM071940 United States
CitationJournal: Commun Biol / Year: 2022
Title: CryoEM structures of anion exchanger 1 capture multiple states of inward- and outward-facing conformations.
Authors: Hristina R Zhekova / Jiansen Jiang / Weiguang Wang / Kirill Tsirulnikov / Gülru Kayık / Hanif Muhammad Khan / Rustam Azimov / Natalia Abuladze / Liyo Kao / Debbie Newman / Sergei Yu Noskov ...Authors: Hristina R Zhekova / Jiansen Jiang / Weiguang Wang / Kirill Tsirulnikov / Gülru Kayık / Hanif Muhammad Khan / Rustam Azimov / Natalia Abuladze / Liyo Kao / Debbie Newman / Sergei Yu Noskov / D Peter Tieleman / Z Hong Zhou / Alexander Pushkin / Ira Kurtz /
Abstract: Anion exchanger 1 (AE1, band 3) is a major membrane protein of red blood cells and plays a key role in acid-base homeostasis, urine acidification, red blood cell shape regulation, and removal of ...Anion exchanger 1 (AE1, band 3) is a major membrane protein of red blood cells and plays a key role in acid-base homeostasis, urine acidification, red blood cell shape regulation, and removal of carbon dioxide during respiration. Though structures of the transmembrane domain (TMD) of three SLC4 transporters, including AE1, have been resolved previously in their outward-facing (OF) state, no mammalian SLC4 structure has been reported in the inward-facing (IF) conformation. Here we present the cryoEM structures of full-length bovine AE1 with its TMD captured in both IF and OF conformations. Remarkably, both IF-IF homodimers and IF-OF heterodimers were detected. The IF structures feature downward movement in the core domain with significant unexpected elongation of TM11. Molecular modeling and structure guided mutagenesis confirmed the functional significance of residues involved in TM11 elongation. Our data provide direct evidence for an elevator-like mechanism of ion transport by an SLC4 family member.
History
DepositionJun 10, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27267.png

Downloads & links

-
Map

FileDownload / File: emd_27267.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain final full map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 192 pix.
= 261.12 Å		1.36 Å/pix.
x 192 pix.
= 261.12 Å		1.36 Å/pix.
x 192 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.064
Minimum - Maximum-0.054245867 - 0.17581543
Average (Standard dev.)0.00025626158 (±0.007508909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Partially connected CD.

Fileemd_27267_additional_1.map
AnnotationPartially connected CD.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Fully connected CD.

Fileemd_27267_additional_2.map
AnnotationFully connected CD.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half1 map.

Fileemd_27267_half_map_1.map
Annotationhalf1 map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2 map.

Fileemd_27267_half_map_2.map
Annotationhalf2 map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : band 3 anion transport protein

EntireName: band 3 anion transport protein
Components
  • Organelle or cellular component: band 3 anion transport protein
    • Protein or peptide: Anion exchange protein

-
Supramolecule #1: band 3 anion transport protein

SupramoleculeName: band 3 anion transport protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 104 KDa

-
Macromolecule #1: Anion exchange protein

MacromoleculeName: Anion exchange protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 104.474258 KDa
SequenceString: MGDPEEYEDQ LEETLEQKEY EDHDSVSIPM EEAEGDTIQE EEAEARVNQL TDTDYHTTSQ HPETHKVCVQ LRELVMDEKN QEIQWMETA RWVGLEENLG KDGIWGRPHL PYLNFWSLLE LQKAFAKGTV LLDLPGKSLA EVANQLLDRF TFEGQIQPDD Q DNLLRVLL ...String:
MGDPEEYEDQ LEETLEQKEY EDHDSVSIPM EEAEGDTIQE EEAEARVNQL TDTDYHTTSQ HPETHKVCVQ LRELVMDEKN QEIQWMETA RWVGLEENLG KDGIWGRPHL PYLNFWSLLE LQKAFAKGTV LLDLPGKSLA EVANQLLDRF TFEGQIQPDD Q DNLLRVLL LKHSHASDME ALGGVKPVVV THSGDPSEPL LPQHPSLETE LFCEQGEGST RGHAPEILGK SPQDWEATLV LV GCARFLK RPVLGFVRLK EPMEPEPKPE GSEEPAVPVR FLIVLLGPEG PNINYTQLGR AAATLMSERV FWNDAYLAQS KET LVQSLE GFLDCSLVLP PLDAPSEKAL LSLVPVQKEL LRRRYLPSPA KPDPSIFKDL DVKKGPGDTP EDPLQRTGKL FGGL VRDIR RRYPRYLSDI TDALSPQVLS AIIFIYFAAL TPAITFGGLL GDKTENMIGV SELLLSTALQ GIIFSLLGAQ PLLVL GFSG PLLVFEEAFY SFCQTNNLEY IVGRVWIGFW LILLVVLVVA FEGSFLVRFI SRYTQEIFSF LISLIFIYET FYKLVT IFQ DHPLQKNYDH DVLTTPKPQA ALPNTALLSL VLMAGTFFLA MMLRKFKNSS YFPGKLRRII GDFGVPISIL IMVMVDA LI QDTYTQKLSV PEGLSVSNPT ERDWLIHPLG IRVEFPIWMM FASALPALLV FILIFLESQI TTLIISKPER KMVKGSGF H LDLLLIIGMG GVGAIFGMPW LSATTVRTVT HANALTVMSK DSTPGAVSQI QGVKEQRISG LLVAVLVGVS ILMGPVLRH IPLAVLFGIF LYMGVTSLSG IQLFDRVLLL LKPRKYYPEV PYARRVKTWR MHLFTITQIV CLVVLWVVRS IKQISLALPF ILILTVPLR RFLLPFIFRD MELKLLDADD VKLNLDEQNG QDEYDEVAMP V

UniProtKB: Anion exchange protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMTris-HClTris Hydrochloride
2.0 CMCPMAL-C8Amphipol-C8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-48 / Average exposure time: 12.0 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 36764 / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.4000000000000001 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

Particle selectionNumber selected: 2635578
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4yzf

Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 251871
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 2)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8d9n:
CryoEM structures of bAE1 captured in multiple states.

+
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