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- EMDB-27431: Cryo-EM structure of Saccharomyces cerevisiae Succinyl-CoA:acetat... -

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Basic information

Entry
Database: EMDB / ID: EMD-27431
TitleCryo-EM structure of Saccharomyces cerevisiae Succinyl-CoA:acetate CoA-transferase (Ach1p)
Map datamap sharp
Sample
  • Complex: Succinyl-CoA:acetate CoA-transferase
    • Protein or peptide: Acetyl-CoA hydrolase
KeywordsAch1p / Succinyl-CoA / acetate CoA-transferase / TRANSFERASE
Function / homology
Function and homology information


acetyl-CoA hydrolase / propionate metabolic process, methylcitrate cycle / acetyl-CoA hydrolase activity / acetate CoA-transferase activity / acetate metabolic process / mitochondrion / cytosol
Similarity search - Function
Acetyl-CoA hydrolase/transferase, N-terminal / Acetyl-CoA hydrolase/transferase C-terminal domain / Acetyl-CoA hydrolase/transferase, C-terminal domain superfamily / Acetyl-CoA hydrolase/transferase N-terminal domain / Acetyl-CoA hydrolase/transferase C-terminal domain / NagB/RpiA transferase-like
Similarity search - Domain/homology
Acetyl-CoA hydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsGodoy AS / Song Y / Cheruvara H / Quigley A / Oliva G
Funding support Brazil, 1 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/07600-3 Brazil
CitationJournal: To Be Published
Title: Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs
Authors: Godoy AS / Song Y / Cheruvara H / Quigley A / Oliva G
History
DepositionJun 25, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27431.png

Downloads & links

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Map

FileDownload / File: emd_27431.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap sharp
Voxel sizeX=Y=Z: 0.831 Å
Density
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.3093894 - 3.5305796
Average (Standard dev.)0.00037902503 (±0.07861526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27431_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: map

Fileemd_27431_additional_1.map
Annotationmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfA

Fileemd_27431_half_map_1.map
AnnotationhalfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27431_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Succinyl-CoA:acetate CoA-transferase

EntireName: Succinyl-CoA:acetate CoA-transferase
Components
  • Complex: Succinyl-CoA:acetate CoA-transferase
    • Protein or peptide: Acetyl-CoA hydrolase

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Supramolecule #1: Succinyl-CoA:acetate CoA-transferase

SupramoleculeName: Succinyl-CoA:acetate CoA-transferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Acetyl-CoA hydrolase

MacromoleculeName: Acetyl-CoA hydrolase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: acetyl-CoA hydrolase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 58.791785 KDa
SequenceString: MTISNLLKQR VRYAPYLKKV KEAHELIPLF KNGQYLGWSG FTGVGTPKAV PEALIDHVEK NNLQGKLRFN LFVGASAGPE ENRWAEHDM IIKRAPHQVG KPIAKAINQG RIEFFDKHLS MFPQDLTYGF YTRERKDNKI LDYTIIEATA IKEDGSIVPG P SVGGSPEF ...String:
MTISNLLKQR VRYAPYLKKV KEAHELIPLF KNGQYLGWSG FTGVGTPKAV PEALIDHVEK NNLQGKLRFN LFVGASAGPE ENRWAEHDM IIKRAPHQVG KPIAKAINQG RIEFFDKHLS MFPQDLTYGF YTRERKDNKI LDYTIIEATA IKEDGSIVPG P SVGGSPEF ITVSDKVIIE VNTATPSFEG IHDIDMPVNP PFRKPYPYLK VDDKCGVDSI PVDPEKVVAI VESTMRDQVP PN TPSDDMS RAIAGHLVEF FRNEVKHGRL PENLLPLQSG IGNIANAVIE GLAGAQFKHL TVWTEVLQDS FLDLFENGSL DYA TATSVR LTEKGFDRAF ANWENFKHRL CLRSQVVSNN PEMIRRLGVI AMNTPVEVDI YAHANSTNVN GSRMLNGLGG SADF LRNAK LSIMHAPSAR PTKVDPTGIS TIVPMASHVD QTEHDLDILV TDQGLADLRG LSPKERAREI INKCAHPDYQ ALLTD YLDR AEHYAKKHNC LHEPHMLKNA FKFHTNLAEK GTMKVDSWEP VD

UniProtKB: Acetyl-CoA hydrolase

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 0.989314222 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hu9

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82557
FSC plot (resolution estimation)

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