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- EMDB-11270: E2 core of the fungal Pyruvate dehydrogenase complex with asymmet... -

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Basic information

Entry
Database: EMDB / ID: EMD-11270
TitleE2 core of the fungal Pyruvate dehydrogenase complex with asymmetric interior PX30 component
Map dataFungal PDC (N. crassa). Recombinant preparation-tE2 PX30. Enforced symmetry: I2. Periphery (PX only) is absent/oversym. Core is structured. Interior is oversymm.
Sample
  • Complex: Core of Pyruvate dehydrogenase complex with asymmetric interior PX component.
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
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: 2.9 Å
AuthorsForsberg BO / Howard RJ / Aibara S / Mortesaei 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: 0.0235
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0235
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zlo
  • Surface level: 0.0235
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zlo
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11270.png

Downloads & links

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Map

FileDownload / File: emd_11270.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFungal PDC (N. crassa). Recombinant preparation-tE2 PX30. Enforced symmetry: I2. Periphery (PX only) is absent/oversym. Core is structured. Interior is oversymm.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 384 pix.
= 430.08 Å		1.12 Å/pix.
x 384 pix.
= 430.08 Å		1.12 Å/pix.
x 384 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0235 / Movie #1: 0.0235
Minimum - Maximum-0.101044826 - 0.19329447
Average (Standard dev.)0.00041953495 (±0.005487489)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 430.08002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z430.080430.080430.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ100115122
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1010.1930.000

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Supplemental data

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Half map: Half-map 1. Fungal PDC (N. crassa). Recombinant preparation-tE2...

Fileemd_11270_half_map_1.map
AnnotationHalf-map 1. Fungal PDC (N. crassa). Recombinant preparation-tE2 PX30. Enforced symmetry: I2. Periphery (PX only) is absent/oversym. Core is structured. Interior is oversymm.
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). Recombinant preparation-tE2...

Fileemd_11270_half_map_2.map
AnnotationHalf-map 2. Fungal PDC (N. crassa). Recombinant preparation-tE2 PX30. Enforced symmetry: I2. Periphery (PX only) is absent/oversym. Core is structured. Interior is oversymm.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Core of Pyruvate dehydrogenase complex with asymmetric interior P...

EntireName: Core of Pyruvate dehydrogenase complex with asymmetric interior PX component.
Components
  • Complex: Core of Pyruvate dehydrogenase complex with asymmetric interior PX component.
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial

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Supramolecule #1: Core of Pyruvate dehydrogenase complex with asymmetric interior P...

SupramoleculeName: Core of Pyruvate dehydrogenase complex with asymmetric interior PX component.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (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: 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: 30.083316 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDRWGSLVPR GSHMAAYTDV PISGMRKTIA ARLKESVTEN PHFFVSTNLS VSKLLKLRQ ALNSSADGRY KLSVNDFLIK AMGIASKRVP TVNSSWRDGV IRQFETVDVS VAVATPNGLI TPIVKGVEGK G LESISAAV ...String:
MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDRWGSLVPR GSHMAAYTDV PISGMRKTIA ARLKESVTEN PHFFVSTNLS VSKLLKLRQ ALNSSADGRY KLSVNDFLIK AMGIASKRVP TVNSSWRDGV IRQFETVDVS VAVATPNGLI TPIVKGVEGK G LESISAAV KELAKKARDG KLKPEEYQGG SISISNMGMN PAVQSFTAII NPPQAAILAV GAPQKVAVPV ENEDGTTGVS WD EQIIVTA SFDHKVVDGA VGAEWIRELK KVIENPLELL L

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

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 27.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129588
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6zlo:
E2 core of the fungal Pyruvate dehydrogenase complex with asymmetric interior PX30 component

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