[English] 日本語
Yorodumi
- EMDB-34290: The cryo-EM structure of hAE2 with bicarbonate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34290
TitleThe cryo-EM structure of hAE2 with bicarbonate
Map data
Sample
  • Complex: hAE2 with bicarbonate
    • Protein or peptide: Anion exchange protein 2
  • Ligand: BICARBONATE IONBicarbonate
Function / homology
Function and homology information


negative regulation of CD8-positive, alpha-beta T cell differentiation / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of enamel mineralization / Bicarbonate transporters / amelogenesis / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transport / digestive tract development ...negative regulation of CD8-positive, alpha-beta T cell differentiation / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of enamel mineralization / Bicarbonate transporters / amelogenesis / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transport / digestive tract development / monoatomic anion transport / regulation of bone resorption / transmembrane transporter activity / osteoclast differentiation / regulation of actin cytoskeleton organization / regulation of intracellular pH / transmembrane transport / spermatogenesis / basolateral plasma membrane / apical plasma membrane / focal adhesion / enzyme binding / membrane / plasma membrane
Similarity search - Function
Anion exchange protein 2 / 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 / Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter family / Phosphotransferase/anion transporter
Similarity search - Domain/homology
Anion exchange protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsZhang Q / Jian L / Yao D / Rao B / Hu K / Xia Y / Cao Y
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFC1004704 China
National Natural Science Foundation of China (NSFC)82072468 China
CitationJournal: Nat Commun / Year: 2023
Title: The structural basis of the pH-homeostasis mediated by the Cl/HCO exchanger, AE2.
Authors: Qing Zhang / Liyan Jian / Deqiang Yao / Bing Rao / Ying Xia / Kexin Hu / Shaobai Li / Yafeng Shen / Mi Cao / An Qin / Jie Zhao / Yu Cao /
Abstract: The cell maintains its intracellular pH in a narrow physiological range and disrupting the pH-homeostasis could cause dysfunctional metabolic states. Anion exchanger 2 (AE2) works at high cellular pH ...The cell maintains its intracellular pH in a narrow physiological range and disrupting the pH-homeostasis could cause dysfunctional metabolic states. Anion exchanger 2 (AE2) works at high cellular pH to catalyze the exchange between the intracellular HCO and extracellular Cl, thereby maintaining the pH-homeostasis. Here, we determine the cryo-EM structures of human AE2 in five major operating states and one transitional hybrid state. Among those states, the AE2 shows the inward-facing, outward-facing, and intermediate conformations, as well as the substrate-binding pockets at two sides of the cell membrane. Furthermore, critical structural features were identified showing an interlock mechanism for interactions among the cytoplasmic N-terminal domain and the transmembrane domain and the self-inhibitory effect of the C-terminal loop. The structural and cell-based functional assay collectively demonstrate the dynamic process of the anion exchange across membranes and provide the structural basis for the pH-sensitive pH-rebalancing activity of AE2.
History
DepositionSep 14, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_34290.png

Downloads & links

-
Map

FileDownload / File: emd_34290.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-6.272768 - 9.730701
Average (Standard dev.)0.00020982456 (±0.16513762)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_34290_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34290_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : hAE2 with bicarbonate

EntireName: hAE2 with bicarbonate
Components
  • Complex: hAE2 with bicarbonate
    • Protein or peptide: Anion exchange protein 2
  • Ligand: BICARBONATE IONBicarbonate

-
Supramolecule #1: hAE2 with bicarbonate

SupramoleculeName: hAE2 with bicarbonate / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137 KDa

-
Macromolecule #1: Anion exchange protein 2

MacromoleculeName: Anion exchange protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137.176906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSAPRRPAK GADSFCTPEP ESLGPGTPGF PEQEEDELHR TLGVERFEEI LQEAGSRGGE EPGRSYGEED FEYHRQSSHH IHHPLSTHL PPDARRRKTP QGPGRKPRRR PGASPTGETP TIEEGEEDED EASEAEGARA LTQPSPVSTP SSVQFFLQED D SADRKAER ...String:
MSSAPRRPAK GADSFCTPEP ESLGPGTPGF PEQEEDELHR TLGVERFEEI LQEAGSRGGE EPGRSYGEED FEYHRQSSHH IHHPLSTHL PPDARRRKTP QGPGRKPRRR PGASPTGETP TIEEGEEDED EASEAEGARA LTQPSPVSTP SSVQFFLQED D SADRKAER TSPSSPAPLP HQEATPRASK GAQAGTQVEE AEAEAVAVAS GTAGGDDGGA SGRPLPKAQP GHRSYNLQER RR IGSMTGA EQALLPRVPT DEIEAQTLAT ADLDLMKSHR FEDVPGVRRH LVRKNAKGST QSGREGREPG PTPRARPRAP HKP HEVFVE LNELLLDKNQ EPQWRETARW IKFEEDVEEE TERWGKPHVA SLSFRSLLEL RRTLAHGAVL LDLDQQTLPG VAHQ VVEQM VISDQIKAED RANVLRALLL KHSHPSDEKD FSFPRNISAG SLGSLLGHHH GQGAESDPHV TEPLMGGVPE TRLEV ERER ELPPPAPPAG ITRSKSKHEL KLLEKIPENA EATVVLVGCV EFLSRPTMAF VRLREAVELD AVLEVPVPVR FLFLLL GPS SANMDYHEIG RSISTLMSDK QFHEAAYLAD EREDLLTAIN AFLDCSVVLP PSEVQGEELL RSVAHFQRQM LKKREEQ GR LLPTGAGLEP KSAQDKALLQ MVEAAGAAED DPLRRTGRPF GGLIRDVRRR YPHYLSDFRD ALDPQCLAAV IFIYFAAL S PAITFGGLLG EKTQDLIGVS ELIMSTALQG VVFCLLGAQP LLVIGFSGPL LVFEEAFFSF CSSNHLEYLV GRVWIGFWL VFLALLMVAL EGSFLVRFVS RFTQEIFAFL ISLIFIYETF YKLVKIFQEH PLHGCSASNS SEVDGGENMT WAGARPTLGP GNRSLAGQS GQGKPRGQPN TALLSLVLMA GTFFIAFFLR KFKNSRFFPG RIRRVIGDFG VPIAILIMVL VDYSIEDTYT Q KLSVPSGF SVTAPEKRGW VINPLGEKSP FPVWMMVASL LPAILVFILI FMETQITTLI ISKKERMLQK GSGFHLDLLL IV AMGGICA LFGLPWLAAA TVRSVTHANA LTVMSKAVAP GDKPKIQEVK EQRVTGLLVA LLVGLSIVIG DLLRQIPLAV LFG IFLYMG VTSLNGIQFY ERLHLLLMPP KHHPDVTYVK KVRTLRMHLF TALQLLCLAL LWAVMSTAAS LAFPFILILT VPLR MVVLT RIFTDREMKC LDANEAEPVF DEREGVDEYN EMPMPV

-
Macromolecule #2: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM / Bicarbonate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 26.0 µm / Nominal defocus min: 10.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 652523
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