[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

TitleCryo-EM structure of human eIF5A-DHS complex reveals the molecular basis of hypusination-associated neurodegenerative disorders.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 1698, Year 2023
Publish dateMar 27, 2023
AuthorsElżbieta Wątor / Piotr Wilk / Artur Biela / Michał Rawski / Krzysztof M Zak / Wieland Steinchen / Gert Bange / Sebastian Glatt / Przemysław Grudnik /
PubMed AbstractHypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The ...Hypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The initial step of hypusination, the formation of deoxyhypusine, is catalyzed by deoxyhypusine synthase (DHS), however, the molecular details of the DHS-mediated reaction remained elusive. Recently, patient-derived variants of DHS and eIF5A have been linked to rare neurodevelopmental disorders. Here, we present the cryo-EM structure of the human eIF5A-DHS complex at 2.8 Å resolution and a crystal structure of DHS trapped in the key reaction transition state. Furthermore, we show that disease-associated DHS variants influence the complex formation and hypusination efficiency. Hence, our work dissects the molecular details of the deoxyhypusine synthesis reaction and reveals how clinically-relevant mutations affect this crucial cellular process.
External linksNat Commun / PubMed:36973244 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.64 - 2.8 Å
Structure data

15052

8a0e

EMDB-15052, PDB-8a0e:
CryoEM structure of DHS-eIF5A1 complex
Method: EM (single particle) / Resolution: 2.8 Å

PDB-7a6s:
Crystal Structure of Asn173Ser variant of Human Deoxyhypusine Synthase
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7a6t:
Crystal Structure of Asn173Ser variant of Human Deoxyhypusine Synthase in complex with NAD and spermidine
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-8a0f:
Crystal structure of human deoxyhypusine synthase variant K329A in complex with NAD and SPD
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-8a0g:
Human deoxyhypusine synthase with trapped transition state
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

Chemicals

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-ACT:
ACETATE ION / Acetate

ChemComp-OXM:
OXAMIC ACID / Oxamic acid

ChemComp-HOH:
WATER / Water

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

ChemComp-SPD:
SPERMIDINE / Spermidine

ChemComp-BME:
BETA-MERCAPTOETHANOL / 2-Mercaptoethanol

ChemComp-MRD:
(4R)-2-METHYLPENTANE-2,4-DIOL / precipitant*YM / 2-Methyl-2,4-pentanediol

ChemComp-13D:
1,3-DIAMINOPROPANE / 1,3-Diaminopropane

Source
  • homo sapiens (human)
KeywordsTRANSFERASE / deoxyhypusine synthase / hypusination / hypusine / translation / neurodegeneration / spermidine dhps deficiency / posttranslational modification

+
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