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- EMDB-11268: E2 core of the fungal Pyruvate dehydrogenase complex with flexibl... -

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Basic information

Entry
Database: EMDB / ID: EMD-11268
TitleE2 core of the fungal Pyruvate dehydrogenase complex with flexible/oversym. periphery, structured core and S4Y-structured interior.
Map dataFungal PDC (N. crassa). Endogenous preparation-E1 E2 E3 PX. Enforced symmetry: T. Periphery is flexible/oversym. Core is structured. Interior is structured in arrangement Y / S4Y.
Sample
  • Complex: endogenous pyruvate dehydrogenase complex form Neurospora crassa
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
    • Protein or peptide: Pyruvate dehydrogenase X component
Keywordsacetyl transferase / pyruvate dehydrogenase / protein complex / mitochondria / metabolism / tetrahedral icosahedral / 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
Similarity search - Component
Biological speciesNeurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsForsberg BO / Aibara S / Howard RJ / Mortezaei N / Lindahl E
Funding support Sweden, European Union, 5 items
OrganizationGrant numberCountry
Swedish Research Council2015-04107 Sweden
Swedish Research Council2017-04641 Sweden
European Research Council (ERC)ERC-2018-StG-805230European Union
European Research Council (ERC)bioexcel-823830European Union
Knut and Alice Wallenberg Foundation2018.0080 Sweden
CitationJournal: Nat Commun / Year: 2020
Title: Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex.
Authors: B O Forsberg / S Aibara / R J Howard / N Mortezaei / E Lindahl /
Abstract: The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) ...The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) of mammalian PDC, PX selectively recruits E3 to the fungal PDC, but its divergent sequence suggests a distinct structural mechanism. Here, we report reconstructions of PDC from the filamentous fungus Neurospora crassa by cryo-electron microscopy, where we find protein X (PX) interior to the PDC core as opposed to substituting E2 core subunits as in mammals. Steric occlusion limits PX binding, resulting in predominantly tetrahedral symmetry, explaining previous observations in Saccharomyces cerevisiae. The PX-binding site is conserved in (and specific to) fungi, and complements possible C-terminal binding motifs in PX that are absent in mammalian E3BP. Consideration of multiple symmetries thus reveals a differential structural basis for E3BP-like function in fungal PDC.
History
DepositionJun 30, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0325
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0325
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zlm
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zlm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11268.png

Downloads & links

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Map

FileDownload / File: emd_11268.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFungal PDC (N. crassa). Endogenous preparation-E1 E2 E3 PX. Enforced symmetry: T. Periphery is flexible/oversym. Core is structured. Interior is structured in arrangement Y / S4Y.
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: 0.0325 / Movie #1: 0.0325
Minimum - Maximum-0.104954585 - 0.22650279
Average (Standard dev.)0.0016335858 (±0.013626762)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000400.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ100115122
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1050.2270.002

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Supplemental data

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Half map: Half-map 1. Fungal PDC (N. crassa). Endogenous preparation-E1...

Fileemd_11268_half_map_1.map
AnnotationHalf-map 1. Fungal PDC (N. crassa). Endogenous preparation-E1 E2 E3 PX. Enforced symmetry: T. Periphery is flexible/oversym. Core is structured. Interior is structured in arrangement Y / S4Y.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2. Fungal PDC (N. crassa). Endogenous preparation-E1...

Fileemd_11268_half_map_2.map
AnnotationHalf-map 2. Fungal PDC (N. crassa). Endogenous preparation-E1 E2 E3 PX. Enforced symmetry: T. Periphery is flexible/oversym. Core is structured. Interior is structured in arrangement Y / S4Y.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : endogenous pyruvate dehydrogenase complex form Neurospora crassa

EntireName: endogenous pyruvate dehydrogenase complex form Neurospora crassa
Components
  • Complex: endogenous pyruvate dehydrogenase complex form Neurospora crassa
    • 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: endogenous pyruvate dehydrogenase complex form Neurospora crassa

SupramoleculeName: endogenous pyruvate dehydrogenase complex form Neurospora crassa
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Catalytic (C-terminal) domain of Dihydrolipoyllysine-residue acetyltransferase (E2-component of pyruvate dehydrogenase complex)
Source (natural)Organism: Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Organelle: mitochondria
Molecular weightTheoretical: 7 MDa

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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: 60 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue acetyltransferase
Source (natural)Organism: Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (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 / Details: Uniprot Q7RWS2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Molecular weightTheoretical: 1.124378 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / 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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 21129
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
FSC plot (resolution estimation)

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