[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

TitleThe unique allosteric property of crocodilian haemoglobin elucidated by cryo-EM.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 6505, Year 2024
Publish dateAug 2, 2024
AuthorsKatsuya Takahashi / Yongchan Lee / Angela Fago / Naim M Bautista / Jay F Storz / Akihiro Kawamoto / Genji Kurisu / Tomohiro Nishizawa / Jeremy R H Tame /
PubMed AbstractThe principal effect controlling the oxygen affinity of vertebrate haemoglobins (Hbs) is the allosteric switch between R and T forms with relatively high and low oxygen affinity respectively. ...The principal effect controlling the oxygen affinity of vertebrate haemoglobins (Hbs) is the allosteric switch between R and T forms with relatively high and low oxygen affinity respectively. Uniquely among jawed vertebrates, crocodilians possess Hb that shows a profound drop in oxygen affinity in the presence of bicarbonate ions. This allows them to stay underwater for extended periods by consuming almost all the oxygen present in the blood-stream, as metabolism releases carbon dioxide, whose conversion to bicarbonate and hydrogen ions is catalysed by carbonic anhydrase. Despite the apparent universal utility of bicarbonate as an allosteric regulator of Hb, this property evolved only in crocodilians. We report here the molecular structures of both human and a crocodilian Hb in the deoxy and liganded states, solved by cryo-electron microscopy. We reveal the precise interactions between two bicarbonate ions and the crocodilian protein at symmetry-related sites found only in the T state. No other known effector of vertebrate Hbs binds anywhere near these sites.
External linksNat Commun / PubMed:39090102 / PubMed Central
MethodsEM (single particle)
Resolution2.2 - 2.35 Å
Structure data

37571
EMDB entry, No image

8wix

EMDB-37571, PDB-8wix:
cryo-EM structure of alligator haemoglobin in carbonmonoxy form
Method: EM (single particle) / Resolution: 2.29 Å

37572
EMDB entry, No image

8wiy

EMDB-37572, PDB-8wiy:
cryo-EM structure of alligator haemoglobin in oxy form
Method: EM (single particle) / Resolution: 2.31 Å

37573
EMDB entry, No image

8wiz

EMDB-37573, PDB-8wiz:
cryo-EM structure of alligator haemoglobin in deoxy form
Method: EM (single particle) / Resolution: 2.2 Å

37574
EMDB entry, No image

8wj0

EMDB-37574, PDB-8wj0:
cryo-EM structure of human haemoglobin in carbonmonoxy form
Method: EM (single particle) / Resolution: 2.24 Å

37575
EMDB entry, No image

8wj1

EMDB-37575, PDB-8wj1:
cryo-EM structure of human haemoglobin in oxy form
Method: EM (single particle) / Resolution: 2.27 Å

37576
EMDB entry, No image

8wj2

EMDB-37576, PDB-8wj2:
cryo-EM structure of human haemoglobin in deoxy form
Method: EM (single particle) / Resolution: 2.35 Å

Chemicals

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-CMO:
CARBON MONOXIDE

ChemComp-HOH:
WATER

ChemComp-OXY:
OXYGEN MOLECULE

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

Source
  • alligator mississippiensis (American alligator)
  • homo sapiens (human)
KeywordsOXYGEN BINDING / Haemoglobin

+
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://pdbjlc1.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