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- EMDB-42284: The structure of the Clostridium thermocellum AdhE spirosome -

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Basic information

Entry
Database: EMDB / ID: EMD-42284
TitleThe structure of the Clostridium thermocellum AdhE spirosome
Map dataMap of the AdhE spirosome
Sample
  • Complex: Homo-oligomer complex of AdhE
    • Protein or peptide: Aldehyde-alcohol dehydrogenase
  • Ligand: FE (III) ION
KeywordsAldehyde-alcohol dehydrogenase / Complex / Spirosome / OXIDOREDUCTASE
Function / homology
Function and homology information


methylglyoxal reductase (NADPH) (acetol producing) activity / butanol dehydrogenase (NAD+) activity / acetaldehyde dehydrogenase (acetylating) activity / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / carbon utilization / metal ion binding / cytosol
Similarity search - Function
Butanol dehydrogenase-like / Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-containing alcohol dehydrogenases signature 2. / 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 ...Butanol dehydrogenase-like / Bifunctional aldehyde-alcohol dehydrogenase / Bifunctional aldehyde-alcohol dehydrogenase, C-terminal domain / Iron-containing alcohol dehydrogenases signature 2. / 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde-alcohol dehydrogenase
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsZiegler SJ / Gruber JN
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Elife / Year: 2024
Title: Structural characterization and dynamics of AdhE ultrastructures from Clostridium thermocellum: A containment strategy for toxic intermediates
Authors: Ziegler S / Knott B / Gruber J / Hengge N / Xu Q / Olson D / Romero E / Joubert L / Bomble Y
History
DepositionOct 9, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42284.png

Downloads & links

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Map

FileDownload / File: emd_42284.map.gz / Format: CCP4 / Size: 266.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the AdhE spirosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 412 pix.
= 337.84 Å		0.82 Å/pix.
x 412 pix.
= 337.84 Å		0.82 Å/pix.
x 412 pix.
= 337.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.029
Minimum - Maximum-0.1703934 - 0.244692
Average (Standard dev.)-0.00000012616374 (±0.010509993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions412412412
Spacing412412412
CellA=B=C: 337.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42284_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_42284_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_42284_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homo-oligomer complex of AdhE

EntireName: Homo-oligomer complex of AdhE
Components
  • Complex: Homo-oligomer complex of AdhE
    • Protein or peptide: Aldehyde-alcohol dehydrogenase
  • Ligand: FE (III) ION

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Supramolecule #1: Homo-oligomer complex of AdhE

SupramoleculeName: Homo-oligomer complex of AdhE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acetivibrio thermocellus DSM 1313 (bacteria)

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Macromolecule #1: Aldehyde-alcohol dehydrogenase

MacromoleculeName: Aldehyde-alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus DSM 1313 (bacteria)
Molecular weightTheoretical: 97.93868 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQGMTKIAN KYEVIDNVEK LEKALKRLRE AQSVYATYTQ EQVDKIFFEA AMAANKMRIP LAKMAVEETG MGVVEDKVI KNHYASEYIY NAYKNTKTCG VIEEDPAFGI KKIAEPLGVI AAVIPTTNPT STAIFKTLIA LKTRNAIIIS P HPRAKNST ...String:
MHHHHHHENL YFQGMTKIAN KYEVIDNVEK LEKALKRLRE AQSVYATYTQ EQVDKIFFEA AMAANKMRIP LAKMAVEETG MGVVEDKVI KNHYASEYIY NAYKNTKTCG VIEEDPAFGI KKIAEPLGVI AAVIPTTNPT STAIFKTLIA LKTRNAIIIS P HPRAKNST IEAAKIVLEA AVKAGAPEGI IGWIDVPSLE LTNLVMREAD VILATGGPGL VKAAYSSGKP AIGVGAGNTP AI IDDSADI VLAVNSIIHS KTFDNGMICA SEQSVIVLDG VYKEVKKEFE KRGCYFLNED ETEKVRKTII INGALNAKIV GQK AHTIAN LAGFEVPETT KILIGEVTSV DISEEFAHEK LCPVLAMYRA KDFDDALDKA ERLVADGGFG HTSSLYIDTV TQKE KLQKF SERMKTCRIL VNTPSSQGGI GDLYNFKLAP SLTLGCGSWG GNSVSDNVGV KHLLNIKTVA ERRENMLWFR TPEKI YIKR GCLPVALDEL KNVMGKKKAF IVTDNFLYNN GYTKPITDKL DEMGIVHKTF FDVSPDPSLA SAKAGAAEML AFQPDT IIA VGGGSAMDAA KIMWVMYEHP EVDFMDMAMR FMDIRKRVYT FPKMGQKAYF IAIPTSAGTG SEVTPFAVIT DEKTGIK YP LADYELLPDM AIVDADMMMN APKGLTAASG IDALTHALEA YVSMLATDYT DSLALRAIKM IFEYLPRAYE NGASDPVA R EKMANAATIA GMAFANAFLG VCHSMAHKLG AFYHLPHGVA NALMINEVIR FNSSEAPTKM GTFPQYDHPR TLERYAEIA DYIGLKGKNN EEKVENLIKA IDELKEKVGI RKTIKDYDID EKEFLDRLDE MVEQAFDDQC TGTNPRYPLM NEIRQMYLNA YYGGAKK

UniProtKB: Aldehyde-alcohol dehydrogenase

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mM(HOCH2)3CNH2Tris
150.0 mMNaClSodium Chloride
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 504494
Startup modelType of model: INSILICO MODEL / In silico model: cylinder generated by RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90912
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8uhw:
The structure of the Clostridium thermocellum AdhE spirosome

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