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- EMDB-14331: Core-binding domain of fungal E3-binding domain bound to the pyru... -

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Basic information

Entry
Database: EMDB / ID: EMD-14331
TitleCore-binding domain of fungal E3-binding domain bound to the pyruvate dehydrogenase E2 core
Map dataPost-processed
Sample
  • Complex: Fungal E3BP bound to PDC E2
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrialDihydrolipoyl transacetylase
    • Protein or peptide: Pyruvate dehydrogenase X component
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / : / glycolytic process
Similarity search - Function
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) ...Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial / Pyruvate dehydrogenase X component
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsForsberg BO
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council2020-06413 Sweden
CitationJournal: Commun Biol / Year: 2023
Title: The structure and evolutionary diversity of the fungal E3-binding protein.
Authors: Bjoern O Forsberg /
Abstract: The pyruvate dehydrogenase complex (PDC) is a central metabolic enzyme in all living cells composed majorly of E1, E2, and E3. Tight coupling of their reactions makes each component essential, so ...The pyruvate dehydrogenase complex (PDC) is a central metabolic enzyme in all living cells composed majorly of E1, E2, and E3. Tight coupling of their reactions makes each component essential, so that any loss impacts oxidative metabolism pathologically. E3 retention is mediated by the E3-binding protein (E3BP), which is here resolved within the PDC core from N.crassa, resolved to 3.2Å. Fungal and mammalian E3BP are shown to be orthologs, arguing E3BP as a broadly eukaryotic gene. Fungal E3BP architectures predicted from sequence data and computational models further bridge the evolutionary distance between N.crassa and humans, and suggest discriminants for E3-specificity. This is confirmed by similarities in their respective E3-binding domains, where an interaction previously not described is also predicted. This provides evolutionary parallels for a crucial interaction human metabolism, an interaction specific to fungi that can be targeted, and an example of protein evolution following gene neofunctionalization.
History
DepositionFeb 11, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14331.png

Downloads & links

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Map

FileDownload / File: emd_14331.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0172
Minimum - Maximum-0.0825726 - 0.13025944
Average (Standard dev.)0.00016102666 (±0.0035866594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14331_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Deepemhancer

Fileemd_14331_additional_1.map
AnnotationDeepemhancer
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_14331_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_14331_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Fungal E3BP bound to PDC E2

EntireName: Fungal E3BP bound to PDC E2
Components
  • Complex: Fungal E3BP bound to PDC E2
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrialDihydrolipoyl transacetylase
    • Protein or peptide: Pyruvate dehydrogenase X component

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Supramolecule #1: Fungal E3BP bound to PDC E2

SupramoleculeName: Fungal E3BP bound to PDC E2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Details: Trimer of the core-binding domain of N.crassa E3-binding protein, interior to icosahedral core assembly of E2 catalytic domains.
Source (natural)Organism: Neurospora crassa (fungus)

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Macromolecule #1: Dihydrolipoyllysine-residue acetyltransferase component of pyruva...

MacromoleculeName: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue acetyltransferase
Source (natural)Organism: Neurospora crassa (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Molecular weightTheoretical: 25.194967 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAYTDVPIS GMRKTIAARL KESVTENPHF FVSTNLSVSK LLKLRQALNS SADGRYKLSV NDFLIKAMGI ASKRVPTVNS SWRDGVIRQ FETVDVSVAV ATPNGLITPI VKGVEGKGLE SISAAVKELA KKARDGKLKP EEYQGGSISI SNMGMNPAVQ S FTAIINPP ...String:
MAAYTDVPIS GMRKTIAARL KESVTENPHF FVSTNLSVSK LLKLRQALNS SADGRYKLSV NDFLIKAMGI ASKRVPTVNS SWRDGVIRQ FETVDVSVAV ATPNGLITPI VKGVEGKGLE SISAAVKELA KKARDGKLKP EEYQGGSISI SNMGMNPAVQ S FTAIINPP QAAILAVGAP QKVAVPVENE DGTTGVSWDE QIIVTASFDH KVVDGAVGAE WIRELKKVIE NPLELLL

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Macromolecule #2: Pyruvate dehydrogenase X component

MacromoleculeName: Pyruvate dehydrogenase X component / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Molecular weightTheoretical: 20.476209 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HHHHHHSQDP NSSPSSENLY FQSPAPPPVA VVTAPISLSA AIDVQNKLHK TIGVFLPLST FITRATEIAN QKLPLPANYQ PTADELFNQ VLGLDKVTRK ESRGSYTPTF GSFVAPQRAA RKADIIDILA APSTRVAASA QSKSAAPGLT TSGPNVFSLQ V PKSEEKRA QAFLQKMKLV LEQEPDKLVR A

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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: 7.5
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: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 31.4 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:

6zlm

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 792478

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7r5m:
Core-binding domain of fungal E3-binding domain bound to the pyruvate dehydrogenase E2 core

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