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- EMDB-0962: The cryo-EM structure of RuBisCO from Anabaena sp. PCC 7120 -

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Basic information

Entry
Database: EMDB / ID: EMD-0962
TitleThe cryo-EM structure of RuBisCO from Anabaena sp. PCC 7120
Map data
Sample
  • Complex: Ternary complex of RuBisCO with chaperone Raf1
    • Other: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
    • Other: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
Biological speciesNostoc sp. PCC 7120 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsXia LY / Jiang YL / Kong WW / Sun H / Li WF / Chen Y / Zhou CZ
Funding support China, 5 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDA24020302 China
Ministry of Science and Technology (MoST, China)2016YFA0400900 China
Ministry of Science and Technology (MoST, China)2018YFA0903100 China
National Natural Science Foundation of China (NSFC)31621002 China
National Natural Science Foundation of China (NSFC)31630001 China
CitationJournal: Nat Plants / Year: 2020
Title: Molecular basis for the assembly of RuBisCO assisted by the chaperone Raf1.
Authors: Ling-Yun Xia / Yong-Liang Jiang / Wen-Wen Kong / Hui Sun / Wei-Fang Li / Yuxing Chen / Cong-Zhao Zhou /
Abstract: The folding and assembly of RuBisCO, the most abundant enzyme in nature, needs a series of chaperones, including the RuBisCO accumulation factor Raf1, which is highly conserved in cyanobacteria and ...The folding and assembly of RuBisCO, the most abundant enzyme in nature, needs a series of chaperones, including the RuBisCO accumulation factor Raf1, which is highly conserved in cyanobacteria and plants. Here, we report the crystal structures of Raf1 from cyanobacteria Anabaena sp. PCC 7120 and its complex with RuBisCO large subunit RbcL. Structural analyses and biochemical assays reveal that each Raf1 dimer captures an RbcL dimer, with the C-terminal tail inserting into the catalytic pocket, and further mediates the assembly of RbcL dimers to form the octameric core of RuBisCO. Furthermore, the cryo-electron microscopy structures of the RbcL-Raf1-RbcS assembly intermediates enable us to see a dynamic assembly process from RbcLRaf1 to the holoenzyme RbcLRbcS. In vitro assays also indicate that Raf1 can attenuate and reverse CcmM-mediated cyanobacterial RuBisCO condensation. Combined with previous findings, we propose a putative model for the assembly of cyanobacterial RuBisCO coordinated by the chaperone Raf1.
History
DepositionJan 16, 2020-
Header (metadata) releaseMay 13, 2020-
Map releaseMay 13, 2020-
UpdateJul 1, 2020-
Current statusJul 1, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0153
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0153
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0962.png

Downloads & links

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Map

FileDownload / File: emd_0962.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.0153 / Movie #1: 0.0153
Minimum - Maximum-0.059501685 - 0.091933325
Average (Standard dev.)0.00019444939 (±0.003629088)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0600.0920.000

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Supplemental data

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Sample components

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Entire : Ternary complex of RuBisCO with chaperone Raf1

EntireName: Ternary complex of RuBisCO with chaperone Raf1
Components
  • Complex: Ternary complex of RuBisCO with chaperone Raf1
    • Other: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
    • Other: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

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Supramolecule #1: Ternary complex of RuBisCO with chaperone Raf1

SupramoleculeName: Ternary complex of RuBisCO with chaperone Raf1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Molecular weightTheoretical: 560 KDa

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Macromolecule #1: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

MacromoleculeName: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN / type: other / ID: 1 / Classification: other
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
SequenceString:
MQTLPKERRY ETLSYLPPLT DVQIEKQVQY ILSQGYIPAV EFNEVSEPTE LYWTLWKLPL FGAKTSREV LAEVQSCRSQ YPGHYIRVVG FDNIKQCQIL SFIVHKPSRY
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Macromolecule #2: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

MacromoleculeName: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN / type: other / ID: 2 / Classification: other
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
SequenceString: MSYAQTKTQT KSGYKAGVQD YRLTYYTPDY TPKDTDILAA FRVTPQPGVP FEEAAAAVAA ESSTGTWTT VWTDLLTDLD RYKGRCYDIE PVPGEDNQFI AYIAYPLDLF EEGSITNVLT S IVGNVFGF KALRALRLED IRFPVAYIKT FQGPPHGIQV ERDKLNKYGR ...String:
MSYAQTKTQT KSGYKAGVQD YRLTYYTPDY TPKDTDILAA FRVTPQPGVP FEEAAAAVAA ESSTGTWTT VWTDLLTDLD RYKGRCYDIE PVPGEDNQFI AYIAYPLDLF EEGSITNVLT S IVGNVFGF KALRALRLED IRFPVAYIKT FQGPPHGIQV ERDKLNKYGR PLLGCTIKPK LG LSAKNYG RAVYECLRGG LDFTKDDENI NSAPFQRWRD RFLFVADAIT KAQAETGEIK GHY LNVTAP TCEEMLKRAE YAKELKQPII MHDYLTAGFT ANTTLARWCR DNGVLLHIHR AMHA VIDRQ KNHGIHFRVL AKALRLSGGD HIHTGTVVGK LEGERGITMG FVDLLRENYV EQDKS RGIY FTQDWASLPG VMAVASGGIH VWHMPALVEI FGDDSVLQFG GGTLGHPWGN APGATA NRV ALEACVQARN EGRNLAREGN DVIREAAKWS PELAVACELW KEIKFEFEAM DTV
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 136934
Details16mer

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Atomic model buiding 1

RefinementProtocol: OTHER

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