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- EMDB-12731: Structure of the repeat unit in the network formed by CcmM full l... -

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Basic information

Entry
Database: EMDB / ID: EMD-12731
TitleStructure of the repeat unit in the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus
Map dataStructure of the repeat unit in the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus
Sample
  • Complex: the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus
Function / homology
Function and homology information


structural constituent of carboxysome shell / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / photosynthesis / monooxygenase activity / magnesium ion binding
Similarity search - Function
Carboxysome assembly protein CcmM / : / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. ...Carboxysome assembly protein CcmM / : / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
Carboxysome assembly protein CcmM / Ribulose bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsZang K / Huping W / Ulrich FH / Manajit HH
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Scaffolding protein CcmM directs multiprotein phase separation in β-carboxysome biogenesis.
Authors: Kun Zang / Huping Wang / F Ulrich Hartl / Manajit Hayer-Hartl /
Abstract: Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural ...Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural biotechnology. Here we analyzed the role of the scaffolding protein CcmM of the β-cyanobacterium Synechococcus elongatus PCC 7942 in sequestrating the hexadecameric Rubisco and the tetrameric carbonic anhydrase, CcaA. We find that the trimeric CcmM, consisting of γCAL oligomerization domains and linked small subunit-like (SSUL) modules, plays a central role in mediation of pre-carboxysome condensate formation through multivalent, cooperative interactions. The γCAL domains interact with the C-terminal tails of the CcaA subunits and additionally mediate a head-to-head association of CcmM trimers. Interestingly, SSUL modules, besides their known function in recruiting Rubisco, also participate in intermolecular interactions with the γCAL domains, providing further valency for network formation. Our findings reveal the mechanism by which CcmM functions as a central organizer of the pre-carboxysome multiprotein matrix, concentrating the core components Rubisco and CcaA before β-carboxysome shell formation.
History
DepositionApr 7, 2021-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12731.png

Downloads & links

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Map

FileDownload / File: emd_12731.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the repeat unit in the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus
Voxel sizeX=Y=Z: 1.885 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.028246587 - 0.08192079
Average (Standard dev.)-2.5558018e-05 (±0.003641119)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 301.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.8851.8851.885
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z301.600301.600301.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0280.082-0.000

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Supplemental data

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Additional map: EM map sharpen by DeepEMhancer

Fileemd_12731_additional_1.map
AnnotationEM map sharpen by DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : the network formed by CcmM full length isoform and Rubisco from S...

EntireName: the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus
Components
  • Complex: the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus

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Supramolecule #1: the network formed by CcmM full length isoform and Rubisco from S...

SupramoleculeName: the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 698820

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