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Yorodumi- EMDB-35536: The cryo-EM structure of eight Rubisco large subunits (RbcL), two... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35536 | |||||||||
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Title | The cryo-EM structure of eight Rubisco large subunits (RbcL), two Arabidopsis thaliana Rubisco accumulation factors 1 (AtRaf1), and seven Arabidopsis thaliana Bundle Sheath Defective 2 (AtBSD2) | |||||||||
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Keywords | Complex / BIOSYNTHETIC PROTEIN / LYASE-CHAPERONE complex | |||||||||
Function / homology | Function and homology information ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone complex / chloroplast stroma / chaperone-mediated protein folding / protein folding chaperone ...ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone complex / chloroplast stroma / chaperone-mediated protein folding / protein folding chaperone / monooxygenase activity / chloroplast / magnesium ion binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) / Synechococcus elongatus PCC 6301 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Wang R / Song H / Zhang W / Wang N / Zhang S / Shao R | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35536.map.gz | 11.2 MB | EMDB map data format | |
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Header (meta data) | emd-35536-v30.xml emd-35536.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_35536.png | 66.1 KB | ||
Filedesc metadata | emd-35536.cif.gz | 6 KB | ||
Others | emd_35536_half_map_1.map.gz emd_35536_half_map_2.map.gz | 98.5 MB 98.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35536 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35536 | HTTPS FTP |
-Validation report
Summary document | emd_35536_validation.pdf.gz | 814.5 KB | Display | EMDB validaton report |
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Full document | emd_35536_full_validation.pdf.gz | 814.1 KB | Display | |
Data in XML | emd_35536_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_35536_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35536 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35536 | HTTPS FTP |
-Related structure data
Related structure data | 8ilmMC 8ilbC 8io2C 8iojC 8iolC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35536.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.076 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35536_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35536_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rubisco assembly intermediate of eight Rubisco large subunits (Rb...
Entire | Name: Rubisco assembly intermediate of eight Rubisco large subunits (RbcL), two Arabidopsis thaliana Rubisco accumulation factors 1 (AtRaf1), and seven Arabidopsis thaliana Bundle Sheath Defective 2 (AtBSD2) |
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Components |
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-Supramolecule #1: Rubisco assembly intermediate of eight Rubisco large subunits (Rb...
Supramolecule | Name: Rubisco assembly intermediate of eight Rubisco large subunits (RbcL), two Arabidopsis thaliana Rubisco accumulation factors 1 (AtRaf1), and seven Arabidopsis thaliana Bundle Sheath Defective 2 (AtBSD2) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Macromolecule #1: Ribulose bisphosphate carboxylase large chain
Macromolecule | Name: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: Synechococcus elongatus PCC 6301 (bacteria) |
Molecular weight | Theoretical: 52.516605 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
Macromolecule | Name: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 8.355468 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAANNNPQGT KPNSLVCANC EGEGCVACSQ CKGGGVNLID HFNGQFKAGA LCWLCRGKKE VLCGDCNGAG FIGGFLSTFD E UniProtKB: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic |
-Macromolecule #3: Rubisco accumulation factor 1.2, chloroplastic
Macromolecule | Name: Rubisco accumulation factor 1.2, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 43.732562 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99991 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: OTHER |