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- EMDB-35605: The Rubisco assembly intermidate of Arabidopsis thaliana Rubisco ... -

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Basic information

Entry
Database: EMDB / ID: EMD-35605
TitleThe Rubisco assembly intermidate of Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) and Rubisco large subunit (RbcL)
Map data
Sample
  • Complex: the complex of RbcL and Raf1 (L8F8)
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Rubisco accumulation factor 1.2, chloroplastic
KeywordsRubisco assembly intermediate / CHAPERONE / LYASE
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast stroma / chloroplast / monooxygenase activity / magnesium ion binding / cytosol
Similarity search - Function
Rubisco accumulation factor 1 / Rubisco accumulation factor 1, helix turn helix domain / Rubisco accumulation factor 1, C-terminal / Rubisco accumulation factor 1, alpha helical domain / Rubisco Assembly chaperone C-terminal domain / Rubisco accumulation factor 1 alpha helical domain / Rubisco accumulation factor 1 helix turn helix domain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. ...Rubisco accumulation factor 1 / Rubisco accumulation factor 1, helix turn helix domain / Rubisco accumulation factor 1, C-terminal / Rubisco accumulation factor 1, alpha helical domain / Rubisco Assembly chaperone C-terminal domain / Rubisco accumulation factor 1 alpha helical domain / Rubisco accumulation factor 1 helix turn helix domain / 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
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / Rubisco accumulation factor 1.2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang R / Song H / Zhang W / Wang N / Zhang S / Shao R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Plant / Year: 2023
Title: Structural insights into the functions of Raf1 and Bsd2 in hexadecameric Rubisco assembly.
Authors: Ran Wang / Hui Song / Wenjuan Zhang / Ning Wang / Shijia Zhang / Ruiqi Shao / Cuimin Liu /
Abstract: Hexadecameric form I Rubisco, which consisting consists of eight large (RbcL) and eight small (RbcS) subunits, is the most abundant enzyme on earth. Extensive efforts to engineer an improved Rubisco ...Hexadecameric form I Rubisco, which consisting consists of eight large (RbcL) and eight small (RbcS) subunits, is the most abundant enzyme on earth. Extensive efforts to engineer an improved Rubisco to speed up its catalytic efficiency and ultimately increase agricultural productivity. However, difficulties with correct folding and assembly in foreign hosts or in vitro have hampered the genetic manipulation of hexadecameric Rubisco. In this study, we reconstituted Synechococcus sp. PCC6301 Rubisco in vitro using the chaperonin system and assembly factors from cyanobacteria and Arabidopsis thaliana (At). Rubisco holoenzyme was produced in the presence of cyanobacterial Rubisco accumulation factor 1 (Raf1) alone or both AtRaf1 and bundle-sheath defective-2 (AtBsd2) from Arabidopsis. RbcL released from GroEL is assembly capable in the presence of ATP, and AtBsd2 functions downstream of AtRaf1. Cryo-EM structures of RbcL-AtRaf1, RbcL-AtRaf1-AtBsd2, and RbcL revealed that the interactions between RbcL and AtRaf1 are looser than those between prokaryotic RbcL and Raf1, with AtRaf1 tilting 7° farther away from RbcL. AtBsd2 stabilizes the flexible regions of RbcL, including the N and C termini, the 60s loop, and loop 6. Using these data, combined with previous findings, we propose the possible biogenesis pathways of prokaryotic and eukaryotic Rubisco.
History
DepositionMar 10, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35605.png

Downloads & links

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Map

FileDownload / File: emd_35605.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.52 Å
Density
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.054957207 - 0.08285309
Average (Standard dev.)0.00013018167 (±0.0031725296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 216.31999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35605_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35605_half_map_2.map
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 complex of RbcL and Raf1 (L8F8)

EntireName: the complex of RbcL and Raf1 (L8F8)
Components
  • Complex: the complex of RbcL and Raf1 (L8F8)
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Rubisco accumulation factor 1.2, chloroplastic

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Supramolecule #1: the complex of RbcL and Raf1 (L8F8)

SupramoleculeName: the complex of RbcL and Raf1 (L8F8) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Ribulose bisphosphate carboxylase large chain

MacromoleculeName: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (bacteria)
Strain: ATCC 27144 / PCC 6301 / SAUG 1402/1
Molecular weightTheoretical: 52.38541 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PKTQSAAGYK AGVKDYKLTY YTPDYTPKDT DLLAAFRFSP QPGVPADEAG AAIAAESSTG TWTTVWTDLL TDMDRYKGKC YHIEPVQGE ENSYFAFIAY PLDLFEEGSV TNILTSIVGN VFGFKAIRSL RLEDIRFPVA LVKTFQGPPH GIQVERDLLN K YGRPMLGC ...String:
PKTQSAAGYK AGVKDYKLTY YTPDYTPKDT DLLAAFRFSP QPGVPADEAG AAIAAESSTG TWTTVWTDLL TDMDRYKGKC YHIEPVQGE ENSYFAFIAY PLDLFEEGSV TNILTSIVGN VFGFKAIRSL RLEDIRFPVA LVKTFQGPPH GIQVERDLLN K YGRPMLGC TIKPKLGLSA KNYGRAVYEC LRGGLDFTKD DENINSQPFQ RWRDRFLFVA DAIHKSQAET GEIKGHYLNV TA PTCEEMM KRAEFAKELG MPIIMHDFLT AGFTANTTLA KWCRDNGVLL HIHRAMHAVI DRQRNHGIHF RVLAKCLRLS GGD HLHSGT VVGKLEGDKA STLGFVDLMR EDHIEADRSR GVFFTQDWAS MPGVLPVASG GIHVWHMPAL VEIFGDDSVL QFGG GTLGH PWGNAPGATA NRVALEACVQ ARNEGRDLYR EGGDILREAG KWSPELAAAL DLWKEIKFEF ETMDKL

UniProtKB: Ribulose bisphosphate carboxylase large chain

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Macromolecule #2: Rubisco accumulation factor 1.2, chloroplastic

MacromoleculeName: Rubisco accumulation factor 1.2, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 38.43673 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SPIPTQFRSL DSAGKIEILA GRMALWFEYA PLISSLYTDG FTPPTIEELT GISSIEQNRL IVGAQVRDSI LQSIHEPELI SAFDTGGAE LLYEIRLLST TQRVAAATFI IDRNIDSKGA QDLARAIKDY PNRRGDVGWL DFDYNLPGDC LSFLYYRQSR E NKNPSDQR ...String:
SPIPTQFRSL DSAGKIEILA GRMALWFEYA PLISSLYTDG FTPPTIEELT GISSIEQNRL IVGAQVRDSI LQSIHEPELI SAFDTGGAE LLYEIRLLST TQRVAAATFI IDRNIDSKGA QDLARAIKDY PNRRGDVGWL DFDYNLPGDC LSFLYYRQSR E NKNPSDQR TSMLLQALGV AESEKAKNRL NTELYGDRIP VVRLKFGEVA EATSVVVLPV CKAEEGEKKI LEAPMEIIAG GD FKVVEAE KGWKRWVVLP SWNPVAAIGK GGVAVSFRDD RKVLPWDGKE EPLLVVADRV RNVVEADDGY YLVVAENGLK LEK GSDLKA REVKESLGMV VLVVRPPRED

UniProtKB: Rubisco accumulation factor 1.2, chloroplastic

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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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 535498

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