[English] 日本語
Yorodumi
- EMDB-18784: CryoEM structure of DHS-eIF5A complex structure from Trichomonas ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18784
TitleCryoEM structure of DHS-eIF5A complex structure from Trichomonas vaginalis
Map data
Sample
  • Complex: Complex of DHS-eIF5A
    • Protein or peptide: Deoxyhypusine synthase related protein, putative
    • Protein or peptide: Eukaryotic translation initiation factor 5A
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: SPERMIDINE
Keywordsparasite / hypusination / eI5FA / hypusine / DHS / Trichomonas vaginalis / deoxyhypusination / translation factor / TRANSLATION
Function / homology
Function and homology information


deoxyhypusine synthase activity / positive regulation of translational termination / positive regulation of translational elongation / translation elongation factor activity / translation initiation factor activity / ribosome binding / RNA binding / cytoplasm
Similarity search - Function
Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal ...Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / DHS-like NAD/FAD-binding domain superfamily / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Deoxyhypusine synthase related protein, putative / Eukaryotic translation initiation factor 5A
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsWator E / Wilk P / Grudnik P
Funding support Poland, 2 items
OrganizationGrant numberCountry
Polish National Science Centre2019/35/N/NZ1/02805 Poland
Polish National Science Centre2019/33/B/NZ1/01839 Poland
CitationJournal: FEBS J / Year: 2024
Title: Structural characterization of the (deoxy)hypusination in Trichomonas vaginalis questions the bifunctionality of deoxyhypusine synthase.
Authors: Elżbieta Wątor / Piotr Wilk / Paweł Kochanowski / Przemysław Grudnik /
Abstract: Trichomonas vaginalis, the causative agent of trichomoniasis, is a prevalent anaerobic protozoan parasite responsible for the most common nonviral sexually transmitted infection globally. While ...Trichomonas vaginalis, the causative agent of trichomoniasis, is a prevalent anaerobic protozoan parasite responsible for the most common nonviral sexually transmitted infection globally. While metronidazole and its derivatives are approved drugs for this infection, rising resistance necessitates the exploration of new antiparasitic therapies. Protein posttranslational modifications (PTMs) play crucial roles in cellular processes, and among them, hypusination, involving eukaryotic translation factor 5A (eIF5A), has profound implications. Despite extensive studies in various organisms, the role of hypusination in T. vaginalis and its potential impact on parasite biology and pathogenicity remain poorly understood. This study aims to unravel the structural basis of the hypusination pathway in T. vaginalis using X-ray crystallography and cryo-electron microscopy. The results reveal high structural homology between T. vaginalis and human orthologs, providing insights into the molecular architecture of eIF5A and deoxyhypusine synthase (DHS) and their interaction. Contrary to previous suggestions of bifunctionality, our analyses indicate that the putative hydroxylation site in tvDHS is nonfunctional, and biochemical assays demonstrate exclusive deoxyhypusination capability. These findings challenge the notion of tvDHS functioning as both deoxyhypusine synthase and hydroxylase. The study enhances understanding of the hypusination pathway in T. vaginalis, shedding light on its functional relevance and potential as a drug target, and contributing to the development of novel therapeutic strategies against trichomoniasis.
History
DepositionOct 30, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18784.png

Downloads & links

-
Map

FileDownload / File: emd_18784.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8456 Å
Density
Contour LevelBy AUTHOR: 0.0754
Minimum - Maximum-0.79729646 - 1.1830137
Average (Standard dev.)-0.00015365235 (±0.025141664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 297.6512 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_18784_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18784_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of DHS-eIF5A

EntireName: Complex of DHS-eIF5A
Components
  • Complex: Complex of DHS-eIF5A
    • Protein or peptide: Deoxyhypusine synthase related protein, putative
    • Protein or peptide: Eukaryotic translation initiation factor 5A
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: SPERMIDINE

-
Supramolecule #1: Complex of DHS-eIF5A

SupramoleculeName: Complex of DHS-eIF5A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Trichomonas vaginalis (eukaryote)

-
Macromolecule #1: Deoxyhypusine synthase related protein, putative

MacromoleculeName: Deoxyhypusine synthase related protein, putative / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Trichomonas vaginalis (eukaryote)
Molecular weightTheoretical: 40.489102 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSRAPSLAPS LAVDSVFVES EELTTPLVKG YVPDDNGKFD FDKMLEQMKY CGFQATNLGL AIDQINEMLH YDYEPQPGDE KKLFGLGGG VEGVKYKPRA CKIFLGITSN LISSGMRDYI RFLVKHALVD VVVCTAGGIE EDFIKCLAPT HMGEFFHDGH D LRKRGLNR ...String:
MSRAPSLAPS LAVDSVFVES EELTTPLVKG YVPDDNGKFD FDKMLEQMKY CGFQATNLGL AIDQINEMLH YDYEPQPGDE KKLFGLGGG VEGVKYKPRA CKIFLGITSN LISSGMRDYI RFLVKHALVD VVVCTAGGIE EDFIKCLAPT HMGEFFHDGH D LRKRGLNR IGNLIVPNKN YCLFEDWIMP ILDKCLEEQN TQGTKWTPSK LIHRLGLEIN NEDSVWYWAA KNNIPVYSPA LT DGSIGDM IYFHSYNNPG LVLDLVEDIR DMNNEPLWAT KTGCIILGGG VVKHHIMNAN LYRNGADFVV YVNTAHDFDG SDS GARPDE AVSWGAISLE AKPVKVYAEV TLVLPLLVAG SFSKFLAE

UniProtKB: Deoxyhypusine synthase related protein, putative

-
Macromolecule #2: Eukaryotic translation initiation factor 5A

MacromoleculeName: Eukaryotic translation initiation factor 5A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trichomonas vaginalis (eukaryote)
Molecular weightTheoretical: 18.430594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSSAEEEVHH DLEIQEVDAG SQEKATIPVN KLKKGGYVLI EGRPCRVVDI TKSKTGKHGH AKAGIAGTDL FTGRRYETHL PTSHEIEVP FVDRSDYGLI NIDDGHTQLL TLDGTLREDV DLPPEGNEMR QRVIDLFNVC VNTNDQVVVT VLSSNGENLI V DCKKSTN

UniProtKB: Eukaryotic translation initiation factor 5A

-
Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

-
Macromolecule #4: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 4 / Number of copies: 3 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 9.3
Component:
ConcentrationFormulaName
200.0 mMNaOH/Glycineglycine buffer
200.0 mMNaClsodium chloride
GridModel: Quantifoil R2/2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Detailsselected images were normalized and low-pass filtered
Particle selectionNumber selected: 1157408 / Details: template picking
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8a0e

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 422161
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5 / Avg.num./class: 100000
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

8a0e


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8qzx:
CryoEM structure of DHS-eIF5A complex structure from Trichomonas vaginalis

+
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://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

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