[English] 日本語
Yorodumi
- EMDB-63004: The complex structure of Halomonas eurihalina BdhE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63004
TitleThe complex structure of Halomonas eurihalina BdhE
Map data
Sample
  • Complex: A tetrameric complex of BdhE
    • Protein or peptide: Aldehyde dehydrogenase family protein
KeywordsComplex / Enzyme / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / metal ion binding
Similarity search - Function
Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain ...Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde dehydrogenase family protein
Similarity search - Component
Biological speciesHalomonas eurihalina (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsKonno N / Miyake K / Nishino S / Omae K / Yanagisawa H / Tsuru S / Kikkawa M / Furusawa C / Iwasaki W
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J20318 Japan
Japan Society for the Promotion of Science (JSPS)24H00870 Japan
Japan Society for the Promotion of Science (JSPS)21H05247 Japan
Japan Society for the Promotion of Science (JSPS)21H05248 Japan
Japan Science and TechnologyJPMJER1902 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121002 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Repeatability of protein structural evolution following convergent gene fusions.
Authors: Naoki Konno / Keita Miyake / Satoshi Nishino / Kimiho Omae / Haruaki Yanagisawa / Saburo Tsuru / Yuki Nishimura / Masahide Kikkawa / Chikara Furusawa / Wataru Iwasaki /
Abstract: Convergent evolution of proteins provides insights into repeatability of genetic adaptation. While local convergence of proteins at residue or domain level has been characterized, global structural ...Convergent evolution of proteins provides insights into repeatability of genetic adaptation. While local convergence of proteins at residue or domain level has been characterized, global structural convergence by inter-domain/molecular interactions remains largely unknown. Here we present structural convergent evolution on fusion enzymes of aldehyde dehydrogenases (ALDHs) and alcohol dehydrogenases (ADHs). We discover BdhE (bifunctional dehydrogenase E), an enzyme clade that emerged independently from the previously known AdhE family through distinct gene fusion events. AdhE and BdhE show shared enzymatic activities and non-overlapping phylogenetic distribution, suggesting common functions in different species. Cryo-electron microscopy reveals BdhEs form donut-like homotetramers, contrasting AdhE's helical homopolymers. Intriguingly, despite distinct quaternary structures and < 30% amino acid sequence identity, both enzymes forms resemble dimeric structure units by ALDH-ADH interactions via convergently elongated loop structures. These findings suggest convergent gene fusions recurrently led to substrate channeling evolution to enhance two-step reaction efficiency. Our study unveils structural convergence at inter-domain/molecular level, expanding our knowledges on patterns behind molecular evolution exploring protein structural universe.
History
DepositionJan 6, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63004.png

Downloads & links

-
Map

FileDownload / File: emd_63004.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 200 pix.
= 206. Å		1.03 Å/pix.
x 200 pix.
= 206. Å		1.03 Å/pix.
x 200 pix.
= 206. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.16985415 - 0.33025217
Average (Standard dev.)0.000456353 (±0.01776675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 206.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_63004_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63004_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : A tetrameric complex of BdhE

EntireName: A tetrameric complex of BdhE
Components
  • Complex: A tetrameric complex of BdhE
    • Protein or peptide: Aldehyde dehydrogenase family protein

-
Supramolecule #1: A tetrameric complex of BdhE

SupramoleculeName: A tetrameric complex of BdhE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Halomonas eurihalina (bacteria)
Molecular weightTheoretical: 377 KDa

-
Macromolecule #1: Aldehyde dehydrogenase family protein

MacromoleculeName: Aldehyde dehydrogenase family protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Halomonas eurihalina (bacteria)
Molecular weightTheoretical: 94.469305 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDSYQLFLDG EFVDAADGRT FTTTDPGNEQ PVATVAQAGE ADALRAIEAA RWAFDHGEWP KMTPQERAAR IYDFADHVTK LAGRLAMAE SMDAGHVINL SKFWAANGAA LLRNLAHYSA NSFPWEEEIP YSGNVGAPGR DYIRREPIGV CVGIIPWNFP A SMAFWKIS ...String:
MDSYQLFLDG EFVDAADGRT FTTTDPGNEQ PVATVAQAGE ADALRAIEAA RWAFDHGEWP KMTPQERAAR IYDFADHVTK LAGRLAMAE SMDAGHVINL SKFWAANGAA LLRNLAHYSA NSFPWEEEIP YSGNVGAPGR DYIRREPIGV CVGIIPWNFP A SMAFWKIS HAIIMGNTIV LKPATQTPLT ALIIAEAAKA AGIPKGVINV ITGQGREVGN LLCTHPDVDK ISFTGSTSVG NN IMKLAAD STKRVTLELG GKSANIILDD ADLDAAVEGA VFGTFLHQGQ VCESGTRLLV SSKIYDAFID KLKARTEALR VGY PLSPES HLGPLVSGKQ LETVEGYVKL GLEEGATLLT GGHRVEVPGI SGGHYYAPTI FTDVDNRMRI AQEEIFGPVV VVIR FDSDE EAVAIANDSI YGLAGGVYSG SNARAQRVAT QLRTGTVWIN NYHAFGDFCP FGGYKQSGFG REMGASGLSE FVQVK RVHV SAYASVGASP AMAILSDDKK TPFVQYNAPT NIISGHGSLP AIYKEMVKLG CKRAVIMTDE GVNATGLPTL VREALD DFC VGVYDRIEQD SSLDTVDAAA AYARECGADA IVSVGGGSVI DTSKAVCVVL KNGGKCNDHM AMLRLQEPQT PHIAIPT TS GTGSEVTNVA VIKNKAVGRK VYILDPHIVP NSTILDPRFT LGLPHRMTVT TALDAMTHSI EALTSTRSQP ICDGQALQ A IRLISENLPR VVAKPHDEAA RANLQLAATM AGWAFNVAQV GLAHAMAHTL GAIHDIPHGL ACGIMLPRVM RFNVDHAGH KLALAAQALG VQTTGMDARE AGLAAAQAVE ALMQSVDHPR YLSDLGVPRD NLSNLAAHAM GDAAIMFNAR PVKGPQEVMA VYEEAY

UniProtKB: Aldehyde dehydrogenase family protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 1.35
Component:
ConcentrationNameFormula
50.0 mMTris-HCl (pH 8.0)
100.0 mMSodium chlorideNaCl
GridMaterial: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
DetailsCircular tetramer

-
Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.75 µm / Nominal defocus min: 1.0 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Predicted by AlphaFold 2.3.2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 667288
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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