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- EMDB-35532: The complexes of RbcL, AtRaf1 and AtBSD2 (LFB) -

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Basic information

Entry
Database: EMDB / ID: EMD-35532
TitleThe complexes of RbcL, AtRaf1 and AtBSD2 (LFB)
Map data
Sample
  • Complex: Rubisco assembly intermidate complex with Syn6301RbcL, AtRaf1 and AtBsd2
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Rubisco accumulation factor 1.2, chloroplastic
    • Protein or peptide: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
KeywordsRUBISCO ASSEMBL INTERMIDATES / COMPLEX / CHAPERONE / LYASE-CHAPERONE complex
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone complex / chloroplast stroma / : / protein folding chaperone ...ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone complex / chloroplast stroma / : / protein folding chaperone / chloroplast / monooxygenase activity / magnesium ion binding / zinc ion binding / cytosol
Similarity search - Function
BSD2 cysteine rich domain / 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 / Heat shock protein DnaJ, cysteine-rich domain superfamily / Ribulose bisphosphate carboxylase large subunit, type I ...BSD2 cysteine rich domain / 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 / Heat shock protein DnaJ, cysteine-rich domain superfamily / 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 / Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic / Rubisco accumulation factor 1.2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Synechococcus elongatus PCC 6301 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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 3, 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_35532.png

Downloads & links

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Map

FileDownload / File: emd_35532.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 288 pix.
= 309.888 Å		1.08 Å/pix.
x 288 pix.
= 309.888 Å		1.08 Å/pix.
x 288 pix.
= 309.888 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.63
Minimum - Maximum-15.435074 - 29.841588999999999
Average (Standard dev.)-0.000000000003731 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 309.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35532_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35532_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Rubisco assembly intermidate complex with Syn6301RbcL, AtRaf1 and...

EntireName: Rubisco assembly intermidate complex with Syn6301RbcL, AtRaf1 and AtBsd2
Components
  • Complex: Rubisco assembly intermidate complex with Syn6301RbcL, AtRaf1 and AtBsd2
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Rubisco accumulation factor 1.2, chloroplastic
    • Protein or peptide: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic

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Supramolecule #1: Rubisco assembly intermidate complex with Syn6301RbcL, AtRaf1 and...

SupramoleculeName: Rubisco assembly intermidate complex with Syn6301RbcL, AtRaf1 and AtBsd2
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 elongatus PCC 6301 (bacteria)
Molecular weightTheoretical: 52.516605 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPKTQSAAGY KAGVKDYKLT YYTPDYTPKD TDLLAAFRFS PQPGVPADEA GAAIAAESST GTWTTVWTDL LTDMDRYKGK CYHIEPVQG EENSYFAFIA YPLDLFEEGS VTNILTSIVG NVFGFKAIRS LRLEDIRFPV ALVKTFQGPP HGIQVERDLL N KYGRPMLG ...String:
MPKTQSAAGY KAGVKDYKLT YYTPDYTPKD TDLLAAFRFS PQPGVPADEA GAAIAAESST GTWTTVWTDL LTDMDRYKGK CYHIEPVQG EENSYFAFIA YPLDLFEEGS VTNILTSIVG NVFGFKAIRS LRLEDIRFPV ALVKTFQGPP HGIQVERDLL N KYGRPMLG CTIKPKLGLS AKNYGRAVYE CLRGGLDFTK DDENINSQPF QRWRDRFLFV ADAIHKSQAE TGEIKGHYLN VT APTCEEM MKRAEFAKEL GMPIIMHDFL TAGFTANTTL AKWCRDNGVL LHIHRAMHAV IDRQRNHGIH FRVLAKCLRL SGG DHLHSG TVVGKLEGDK ASTLGFVDLM REDHIEADRS RGVFFTQDWA SMPGVLPVAS GGIHVWHMPA LVEIFGDDSV LQFG GGTLG HPWGNAPGAT ANRVALEACV QARNEGRDLY REGGDILREA GKWSPELAAA LDLWKEIKFE FETMDKL

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 43.732562 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MQQLYQPFRP PSSPIPTQFR SLDSAGKIEI LAGRMALWFE YAPLISSLYT DGFTPPTIEE LTGISSIEQN RLIVGAQVRD SILQSIHEP ELISAFDTGG AELLYEIRLL STTQRVAAAT FIIDRNIDSK GAQDLARAIK DYPNRRGDVG WLDFDYNLPG D CLSFLYYR ...String:
MQQLYQPFRP PSSPIPTQFR SLDSAGKIEI LAGRMALWFE YAPLISSLYT DGFTPPTIEE LTGISSIEQN RLIVGAQVRD SILQSIHEP ELISAFDTGG AELLYEIRLL STTQRVAAAT FIIDRNIDSK GAQDLARAIK DYPNRRGDVG WLDFDYNLPG D CLSFLYYR QSRENKNPSD QRTSMLLQAL GVAESEKAKN RLNTELYGDK EAEKEKEKKK KEEEVKAIRI PVVRLKFGEV AE ATSVVVL PVCKAEEGEK KILEAPMEII AGGDFKVVEA EKGWKRWVVL PSWNPVAAIG KGGVAVSFRD DRKVLPWDGK EEP LLVVAD RVRNVVEADD GYYLVVAENG LKLEKGSDLK AREVKESLGM VVLVVRPPRE DDDDWQTSHQ NWD

UniProtKB: Rubisco accumulation factor 1.2, chloroplastic

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Macromolecule #3: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic

MacromoleculeName: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 8.355468 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAANNNPQGT KPNSLVCANC EGEGCVACSQ CKGGGVNLID HFNGQFKAGA LCWLCRGKKE VLCGDCNGAG FIGGFLSTFD E

UniProtKB: Protein BUNDLE SHEATH DEFECTIVE 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 233489
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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