[English] 日本語
Yorodumi
- EMDB-63003: The complex structure of Escherichia coli AdhE (compact conformation) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63003
TitleThe complex structure of Escherichia coli AdhE (compact conformation)
Map data
Sample
  • Complex: A structural unit of compact-form helical polymers formed by AdhE
    • Protein or peptide: Bifunctional aldehyde-alcohol dehydrogenase AdhE
KeywordsComplex / Enzyme / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


ethanol biosynthetic process / mixed acid fermentation / acetaldehyde dehydrogenase (acetylating) / ethanol dehydrogenase (NAD+) activity / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / ferrous iron binding / protein homooligomerization ...ethanol biosynthetic process / mixed acid fermentation / acetaldehyde dehydrogenase (acetylating) / ethanol dehydrogenase (NAD+) activity / acetaldehyde dehydrogenase (acetylating) activity / carbon utilization / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / ferrous iron binding / protein homooligomerization / response to oxidative stress / identical protein binding / membrane / cytosol
Similarity search - Function
Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / 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 ...Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-type alcohol dehydrogenase-like / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Bifunctional aldehyde-alcohol dehydrogenase AdhE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 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: To Be Published
Title: Repeatability of protein structural evolution following convergent gene fusions
Authors: Konno N / Miyake K / Nishino S / Omae K / Yanagisawa H / Tsuru S / Kikkawa M / Furusawa C / Iwasaki W
History
DepositionJan 6, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63003.png

Downloads & links

-
Map

FileDownload / File: emd_63003.map.gz / Format: CCP4 / Size: 67 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 260 pix.
= 267.8 Å		1.03 Å/pix.
x 260 pix.
= 267.8 Å		1.03 Å/pix.
x 260 pix.
= 267.8 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: 0.04
Minimum - Maximum-0.07395388 - 0.2161876
Average (Standard dev.)0.00051504874 (±0.009538321)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 267.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_63003_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_63003_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63003_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : A structural unit of compact-form helical polymers formed by AdhE

EntireName: A structural unit of compact-form helical polymers formed by AdhE
Components
  • Complex: A structural unit of compact-form helical polymers formed by AdhE
    • Protein or peptide: Bifunctional aldehyde-alcohol dehydrogenase AdhE

-
Supramolecule #1: A structural unit of compact-form helical polymers formed by AdhE

SupramoleculeName: A structural unit of compact-form helical polymers formed by AdhE
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 386.42 KDa

-
Macromolecule #1: Bifunctional aldehyde-alcohol dehydrogenase AdhE

MacromoleculeName: Bifunctional aldehyde-alcohol dehydrogenase AdhE / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: acetaldehyde dehydrogenase (acetylating)
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 96.244117 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAVTNVAELN ALVERVKKAQ REYASFTQEQ VDKIFRAAAL AAADARIPLA KMAVAESGMG IVEDKVIKNH FASEYIYNAY KDEKTCGVL SEDDTFGTIT IAEPIGIICG IVPTTNPTST AIFKSLISLK TRNAIIFSPH PRAKDATNKA ADIVLQAAIA A GAPKDLIG ...String:
MAVTNVAELN ALVERVKKAQ REYASFTQEQ VDKIFRAAAL AAADARIPLA KMAVAESGMG IVEDKVIKNH FASEYIYNAY KDEKTCGVL SEDDTFGTIT IAEPIGIICG IVPTTNPTST AIFKSLISLK TRNAIIFSPH PRAKDATNKA ADIVLQAAIA A GAPKDLIG WIDQPSVELS NALMHHPDIN LILATGGPGM VKAAYSSGKP AIGVGAGNTP VVIDETADIK RAVASVLMSK TF DNGVICA SEQSVVVVDS VYDAVRERFA THGGYLLQGK ELKAVQDVIL KNGALNAAIV GQPAYKIAEL AGFSVPENTK ILI GEVTVV DESEPFAHEK LSPTLAMYRA KDFEDAVEKA EKLVAMGGIG HTSCLYTDQD NQPARVSYFG QKMKTARILI NTPA SQGGI GDLYNFKLAP SLTLGCGSWG GNSISENVGP KHLINKKTVA KRAENMLWHK LPKSIYFRRG SLPIALDEVI TDGHK RALI VTDRFLFNNG YADQITSVLK AAGVETEVFF EVEADPTLSI VRKGAELANS FKPDVIIALG GGSPMDAAKI MWVMYE HPE THFEELALRF MDIRKRIYKF PKMGVKAKMI AVTTTSGTGS EVTPFAVVTD DATGQKYPLA DYALTPDMAI VDANLVM DM PKSLCAFGGL DAVTHAMEAY VSVLASEFSD GQALQALKLL KEYLPASYHE GSKNPVARER VHSAATIAGI AFANAFLG V CHSMAHKLGS QFHIPHGLAN ALLICNVIRY NANDNPTKQT AFSQYDRPQA RRRYAEIADH LGLSAPGDRT AAKIEKLLA WLETLKAELG IPKSIREAGV QEADFLANVD KLSEDAFDDQ CTGANPRYPL ISELKQILLD TYYGRDYVEG ETAAKKEAAP AKAEKKAKK SA

UniProtKB: Bifunctional aldehyde-alcohol dehydrogenase AdhE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

Concentration2.02 mg/mL
BufferpH: 8
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

-
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: PDB ENTRY
PDB model - PDB ID:

6tqm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 804190
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