[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleArchitecture of the human erythrocyte ankyrin-1 complex.
Journal, issue, pagesNat Struct Mol Biol, Vol. 29, Issue 7, Page 706-718, Year 2022
Publish dateJul 14, 2022
AuthorsFrancesca Vallese / Kookjoo Kim / Laura Y Yen / Jake D Johnston / Alex J Noble / Tito Calì / Oliver Biggs Clarke /
PubMed AbstractThe stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association ...The stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association with the band 3 anion exchanger and the Rhesus glycoproteins remains unknown. Here we present structures of ankyrin-1 complexes purified from human erythrocytes. We reveal the architecture of a core complex of ankyrin-1, the Rhesus proteins RhAG and RhCE, the band 3 anion exchanger, protein 4.2, glycophorin A and glycophorin B. The distinct T-shaped conformation of membrane-bound ankyrin-1 facilitates recognition of RhCE and, unexpectedly, the water channel aquaporin-1. Together, our results uncover the molecular details of ankyrin-1 association with the erythrocyte membrane, and illustrate the mechanism of ankyrin-mediated membrane protein clustering.
External linksNat Struct Mol Biol / PubMed:35835865 / PubMed Central
MethodsEM (single particle) / EM (subtomogram averaging)
Resolution2.17 - 25.0 Å
Structure data

EMDB-26874, PDB-7uz3:
Band 3-Glycophorin A complex, outward facing
Method: EM (single particle) / Resolution: 2.35 Å

EMDB-26886, PDB-7uze:
Erythrocyte ankyrin-1 complex class 2 local refinement of AQP1 (C4 symmetry applied)
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-26916, PDB-7uzq:
Local refinement of RhAG-RhCE-ANK1(AR1-5), from consensus refinement of all classes
Method: EM (single particle) / Resolution: 2.17 Å

EMDB-26917, PDB-7uzs:
Protein 4.2 (local refinement from consensus reconstruction of ankyrin complex classes)
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-26918, PDB-7uzu:
Ankyrin-1 (N-terminal region of membrane binding domain, local refinement from consensus reconstruction; bound to N-terminal peptide from band 3)
Method: EM (single particle) / Resolution: 2.3 Å

EMDB-26919, PDB-7uzv:
Cytoplasmic domains of Band 3-I (local refinement from consensus reconstruction of ankyrin complexes)
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-26940, PDB-7v07:
Band 3-I-TM local refinement from erythrocyte ankyrin-1 complex consensus reconstruction
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-26943, PDB-7v0k:
Consensus refinement of human erythrocyte ankyrin-1 complex (Composite map)
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-26944, PDB-7v0m:
Local refinement of ankyrin-1 (N-terminal half), class 1 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-26948, PDB-7v0q:
Local refinement of protein 4.2, class 1 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-26949, PDB-7v0s:
Local refinement of RhAG/CE trimer, class 1 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-26950, PDB-7v0t:
Local refinement of Band 3-I cytoplasmic domains, class 1 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-26951, PDB-7v0u:
Local refinement of Band 3-II cytoplasmic domains, class 1 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-26952, PDB-7v0x:
Local refinement of ankyrin-1 (C-terminal half), class 1 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-26953, PDB-7v0y:
Local refinement of Band 3-III cytoplasmic domains, class 1 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-26954, PDB-7v19:
Local refinement of Band 3-II transmembrane domains, class 1 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-26955, PDB-8crq:
Local refinement of Band 3-I transmembrane domains, class 1 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-26956, PDB-8crr:
Local refinement of Band 3-III transmembrane domains, class 1 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-26958, PDB-8crt:
Local refinement of Rh trimer, glycophorin B and Band3-III transmembrane region, class 1a of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-26960, PDB-8cs9:
Composite reconstruction of Class 1 of the erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 2.74 Å

EMDB-26965, PDB-8csl:
Sub-tomogram averaging of erythrocyte ankyrin-1 complex
Method: EM (subtomogram averaging) / Resolution: 25.0 Å

EMDB-26972, PDB-8csv:
Local refinement of Anykyrin-1 (N-terminal half of membrane binding domain) in Class 2 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-26973, PDB-8csw:
Local refinement of protein 4.2 in Class 2 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-26974, PDB-8csx:
Local refinement of RhAG/CE trimer in class 2 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-26975, PDB-8csy:
Local refinement of cytoplasmic domains of band3-I in class 2 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-26978, PDB-8ct2:
Local refinement of AQP1 tetramer (C1; refinement mask included D1 of protein 4.2 and Ankyrin-1 AR1-5) in Class 2 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-26979, PDB-8ct3:
Local refinement of band3-I transmembrane region from class 2 of erythrocyte ankyrin-1 complex
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-26988, PDB-8cte:
Class 2 of erythrocyte ankyrin-1 complex (Composite map)
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-CLR:
CHOLESTEROL

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

ChemComp-HOH:
WATER

ChemComp-AJP:
Digitonin / detergent*YM

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

Source
  • homo sapiens (human)
  • human (human)
KeywordsTRANSPORT PROTEIN / Membrane Protein / Anion Exchange / Erythrocyte / Glycoprotein / STRUCTURAL PROTEIN / Ankyrin / TRANSPORT PROTEIN/STRUCTURAL PROTEIN / TRANSPORT PROTEIN-STRUCTURAL PROTEIN complex / ankyrin complex

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more