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- EMDB-28847: 3-methylcrotonyl-CoA carboxylase in filaments, filament termini -

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Basic information

Entry
Database: EMDB / ID: EMD-28847
Title3-methylcrotonyl-CoA carboxylase in filaments, filament termini
Map datamcc, filament termini map
Sample
  • Complex: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament
Keywordsenzyme / multienzyme / multi-enzyme / biotin-dependent / leucine catabolism / PROTEIN FIBRIL
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsHu JJ / Lee JKJ / Liu YT / Yu C / Huang L / Afasizheva I / Afasizhev R / Zhou ZH
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI101057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM074830 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Science Foundation (NSF, United States)DBI-133813 United States
Citation
Journal: Structure / Year: 2023
Title: Discovery, structure, and function of filamentous 3-methylcrotonyl-CoA carboxylase.
Authors: Jason J Hu / Jane K J Lee / Yun-Tao Liu / Clinton Yu / Lan Huang / Inna Aphasizheva / Ruslan Aphasizhev / Z Hong Zhou /
Abstract: 3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been ...3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been characterized, the structure and potential polymerization of native MCC remain elusive. Here, we discovered that native MCC from Leishmania tarentolae (LtMCC) forms filaments, and determined the structures of different filament regions at 3.4, 3.9, and 7.3 Å resolution using cryoEM. αβ LtMCCs assemble in a twisted-stacks architecture, manifesting as supramolecular rods up to 400 nm. Filamentous LtMCCs bind biotin non-covalently and lack coenzyme A. Filaments elongate by stacking αβ LtMCCs onto the exterior α-trimer of the terminal LtMCC. This stacking immobilizes the biotin carboxylase domains, sequestering the enzyme in an inactive state. Our results support a new model for LtMCC catalysis, termed the dual-swinging-domains model, and cast new light on the function of polymerization in the carboxylase superfamily and beyond.
#1: Journal: To Be Published
Title: Discovery, Structure, and Function of Filamentous 3-Methylcrotonyl-CoA Carboxylase
Authors: Hu JJ / Lee JKJ / Liu YT / Yu C / Huang L / Afasizheva I / Afasizhev R / Zhou ZH
History
DepositionNov 9, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28847.png

Downloads & links

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Map

FileDownload / File: emd_28847.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmcc, filament termini map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 384 pix.
= 417.408 Å		1.09 Å/pix.
x 384 pix.
= 417.408 Å		1.09 Å/pix.
x 384 pix.
= 417.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.014210542 - 0.03239438
Average (Standard dev.)0.00014158392 (±0.0021838988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 417.40802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: mcc, filament termini map, half1

Fileemd_28847_half_map_1.map
Annotationmcc, filament termini map, half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: mcc, filament termini map, half2

Fileemd_28847_half_map_2.map
Annotationmcc, filament termini map, half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament

EntireName: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament
Components
  • Complex: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament

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Supramolecule #1: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament

SupramoleculeName: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: TATII/UC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3380
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

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