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- EMDB-16884: Core-binding domain of fungal E3-binding domain bound to the nati... -

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Basic information

Entry
Database: EMDB / ID: EMD-16884
TitleCore-binding domain of fungal E3-binding domain bound to the native pyruvate dehydrogenase E2 core
Map dataN. crassa native PDC core with E3BP interior trimer
Sample
  • Complex: Native pyruvate dehydrogenase complex
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
    • Protein or peptide: Pyruvate dehydrogenase X component
KeywordsComplex / metabolism / mitochondria / TRANSFERASE
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / mitochondrial matrix
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: 4.1 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
DepositionMar 21, 2023-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16884.png

Downloads & links

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Map

FileDownload / File: emd_16884.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationN. crassa native PDC core with E3BP interior trimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 320 pix.
= 400. Å		1.25 Å/pix.
x 320 pix.
= 400. Å		1.25 Å/pix.
x 320 pix.
= 400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.07476227 - 0.18085432
Average (Standard dev.)0.0007885768 (±0.0074057863)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16884_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16884_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native pyruvate dehydrogenase complex

EntireName: Native pyruvate dehydrogenase complex
Components
  • Complex: Native pyruvate dehydrogenase complex
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
    • Protein or peptide: Pyruvate dehydrogenase X component

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Supramolecule #1: Native pyruvate dehydrogenase complex

SupramoleculeName: Native pyruvate dehydrogenase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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)
Molecular weightTheoretical: 48.677395 KDa
SequenceString: MIVPVLSRQA LRHASVARVA LPSLTRWYAS YPPHTVVKMP ALSPTMTSGG IGAWQKKPGD KIEPGEVLVE IETDKAQMDF EFQEEGVLA KILKDSGEKD VAVGNPIAIL VEEGTDVNAF KDFTLKDAGG ETSPAVPKDE PKNESTASAP TPAPTPAPEP E NTSFTGRF ...String:
MIVPVLSRQA LRHASVARVA LPSLTRWYAS YPPHTVVKMP ALSPTMTSGG IGAWQKKPGD KIEPGEVLVE IETDKAQMDF EFQEEGVLA KILKDSGEKD VAVGNPIAIL VEEGTDVNAF KDFTLKDAGG ETSPAVPKDE PKNESTASAP TPAPTPAPEP E NTSFTGRF QTALEREPNA LPAAKRLARE KGIDLRNVKG SGPGGKITEE DVKKALASAP AAGAAAAAYT DVPISGMRKT IA ARLKESV TENPHFFVST NLSVSKLLKL RQALNSSADG RYKLSVNDFL IKAMGIASKR VPTVNSSWRD GVIRQFETVD VSV AVATPN GLITPIVKGV EGKGLESISA AVKELAKKAR DGKLKPEEYQ GGSISISNMG MNPAVQSFTA IINPPQAAIL AVGA PQKVA VPVENEDGTT GVSWDEQIIV TASFDHKVVD GAVGAEWIRE LKKVIENPLE LLL

UniProtKB: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial

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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)
Molecular weightTheoretical: 44.880066 KDa
SequenceString: MASLTAACRI SARMAGRSVR GFRTSAAALA AQNFTMPALS PTMTEGNIAT WRVKEGDKFS AGDVLLEIET DKATMDVEAQ DDGVMVKIM KNDGAKGVAV GARIAVIAEE GDDISSLEIP ADAAPQSKPA ESAPSAPPPP TTADQSNVAV PESAPQNASS K SAPKPPKR ...String:
MASLTAACRI SARMAGRSVR GFRTSAAALA AQNFTMPALS PTMTEGNIAT WRVKEGDKFS AGDVLLEIET DKATMDVEAQ DDGVMVKIM KNDGAKGVAV GARIAVIAEE GDDISSLEIP ADAAPQSKPA ESAPSAPPPP TTADQSNVAV PESAPQNASS K SAPKPPKR QYPHYPSVAH LLKVNGIDAA AVKDITPTGP GGRLLKGDVL AYLGKINAQT PSTVSERFEK QSHLDLSNIK VA KSTEAVK ATTEKAQSKK LDAPAPPPVA VVTAPISLSA AIDVQNKLHK TIGVFLPLST FITRATEIAN QKLPLPANYQ PTA DELFNQ VLGLDKVTRK ESRGSYTPTF GSFVAPQRAA RKADIIDILA APSTRVAASA QSKSAAPGLT TSGPNVFSLQ VPKS EEKRA QAFLQKMKLV LEQEPDKLVR A

UniProtKB: Pyruvate dehydrogenase X component

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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 TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

11267

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 604402
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChain

7r5m

chain_id: A, source_name: PDB, initial_model_type: experimental model

7r5m

chain_id: C, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8ohs:
Core-binding domain of fungal E3-binding domain bound to the native pyruvate dehydrogenase E2 core

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