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Yorodumi- EMDB-37903: Cryo-EM map of the intact alpha-carboxysome from Prochlorococcus MED4 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37903 | ||||||||||||||||||
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Title | Cryo-EM map of the intact alpha-carboxysome from Prochlorococcus MED4 | ||||||||||||||||||
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Sample |
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Keywords | alpha-carboxysome / carbon fixation / PHOTOSYNTHESIS | ||||||||||||||||||
Biological species | Prochlorococcus (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.5 Å | ||||||||||||||||||
Authors | Jiang YL / Zhou RQ / Zhou CZ / Zeng QL | ||||||||||||||||||
Funding support | China, Hong Kong, 5 items
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Citation | Journal: Nat Plants / Year: 2024 Title: Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus. Authors: Rui-Qian Zhou / Yong-Liang Jiang / Haofu Li / Pu Hou / Wen-Wen Kong / Jia-Xin Deng / Yuxing Chen / Cong-Zhao Zhou / Qinglu Zeng / Abstract: Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self- ...Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self-assembly principles of the intact carboxysome remain elusive. Here we purified α-carboxysomes from Prochlorococcus and examined their intact structures using single-particle cryo-electron microscopy to solve the basic principles of their shell construction and internal RuBisCO organization. The 4.2 Å icosahedral-like shell structure reveals 24 CsoS1 hexamers on each facet and one CsoS4A pentamer at each vertex. RuBisCOs are organized into three concentric layers within the shell, consisting of 72, 32 and up to 4 RuBisCOs at the outer, middle and inner layers, respectively. We uniquely show how full-length and shorter forms of the scaffolding protein CsoS2 bind to the inner surface of the shell via repetitive motifs in the middle and C-terminal regions. Combined with previous reports, we propose a concomitant 'outside-in' assembly principle of α-carboxysomes: the inner surface of the self-assembled shell is reinforced by the middle and C-terminal motifs of the scaffolding protein, while the free N-terminal motifs cluster to recruit RuBisCO in concentric, three-layered spherical arrangements. These new insights into the coordinated assembly of α-carboxysomes may guide the rational design and repurposing of carboxysome structures for improving plant photosynthetic efficiency. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37903.map.gz | 828.6 MB | EMDB map data format | |
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Header (meta data) | emd-37903-v30.xml emd-37903.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
Images | emd_37903.png | 53.5 KB | ||
Filedesc metadata | emd-37903.cif.gz | 6.3 KB | ||
Others | emd_37903_half_map_1.map.gz emd_37903_half_map_2.map.gz | 2.7 GB 2.7 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37903 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37903 | HTTPS FTP |
-Validation report
Summary document | emd_37903_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_37903_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_37903_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | emd_37903_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37903 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37903 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_37903.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37903_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37903_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : alpha-carboxysome
Entire | Name: alpha-carboxysome |
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Components |
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-Supramolecule #1: alpha-carboxysome
Supramolecule | Name: alpha-carboxysome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Prochlorococcus (bacteria) |
Molecular weight | Theoretical: 97.5 MDa |
-Macromolecule #1: RuBisCO
Macromolecule | Name: RuBisCO / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Prochlorococcus (bacteria) |
Sequence | String: MSKKYDAGVK EYRDTYWTPE YVPLDTDLLA CFKCTGQEGV PREEVAAAVA AESSTGTWST VWSELLTDL EFYKGRCYRI EDVPGDPEAF YAFIAYPLDL FEEGSITNVL TSLVGNVFGF K ALRHLRLE DIRFPIAFIK TCGGPPNGIV VERDRLNKYG RPLLGCTIKP ...String: MSKKYDAGVK EYRDTYWTPE YVPLDTDLLA CFKCTGQEGV PREEVAAAVA AESSTGTWST VWSELLTDL EFYKGRCYRI EDVPGDPEAF YAFIAYPLDL FEEGSITNVL TSLVGNVFGF K ALRHLRLE DIRFPIAFIK TCGGPPNGIV VERDRLNKYG RPLLGCTIKP KLGLSGKNYG RV VYECLRG GLDLTKDDEN INSQPFQRWR ERFEFVAEAV KLAQQETGEV KGHYLNCTAN TPE ELYERA EFAKELDMPI IMHDYITGGF TANTGLANWC RKNGMLLHIH RAMHAVIDRH PKHG IHFRV LAKCLRLSGG DQLHTGTVVG KLEGDRQTTL GYIDNLRESF VPEDRSRGNF FDQDW GSMP GVFAVASGGI HVWHMPALLA IFGDDSCLQF GGGTHGHPWG SAAGAAANRV ALEACV KAR NAGREIEKES RDILMEAAKH SPELAIALET WKEIKFEFDT VDKLDVQG M PFQSSVGDYQ TVATLETFGF LPPMTQEEIY DQIAYIIAQG WSPVIEHVHP SGSMQTYWS YWKLPFFGEK DLNLVVSELE ACHRAYPDHH VRIIGYDAYT QSQGTAFAVF QGR |
-Macromolecule #2: the shell hexamer CsoS1
Macromolecule | Name: the shell hexamer CsoS1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Prochlorococcus (bacteria) |
Sequence | String: MGIALGMIET RGLVPAIEAA DAMTKAAEVR LIGREFVGGG YVTVLVRGET GAVNA AVRA GADACERVGD GLVAAHIIAR PHREVEPALG NGDFLGQKD |
-Macromolecule #3: the shell trimer CsoS1D
Macromolecule | Name: the shell trimer CsoS1D / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Prochlorococcus (bacteria) |
Sequence | String: MEPTSSLNRG DRKKGSSLVT GSEVQSQSNG ASCFITTDSE KSLVSRQASQ VEQIELRTYV FLDSLQPQL AAYMGTVSRG FLPIPGDSCL WMEVSPGMAV HRVTDIALKA SNVRLGQMIV E RAFGSLAL YHKDQSTVLH SGDVVLDAIG SEVRKRTKPS TSWTEVICAI ...String: MEPTSSLNRG DRKKGSSLVT GSEVQSQSNG ASCFITTDSE KSLVSRQASQ VEQIELRTYV FLDSLQPQL AAYMGTVSRG FLPIPGDSCL WMEVSPGMAV HRVTDIALKA SNVRLGQMIV E RAFGSLAL YHKDQSTVLH SGDVVLDAIG SEVRKRTKPS TSWTEVICAI TPDHAVLINR QN RSGSMIQ SGMSMFILET EPAGYVLKAA NEAEKSANIT IIDVKAVGAF GRLTLAGKEG DVE EAAAAA IRAIDQISNY |
-Macromolecule #4: the shell pentamer CsoS4A
Macromolecule | Name: the shell pentamer CsoS4A / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Prochlorococcus (bacteria) |
Sequence | String: MLICKVLKPL VSTNRIPGFE HKHLQVVLDG SSNKVAVDAV GCKPGDWVIC VGSSAAREAA GSKSYPSDL TIVGIIDHWD PDSPKQIEV |
-Macromolecule #5: The shell pentamer CsoS4B
Macromolecule | Name: The shell pentamer CsoS4B / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Prochlorococcus (bacteria) |
Sequence | String: MVCTQRVAGL GHMNLRILEN NKGKKVVAVD PVGAREGNWV FTASGSAARF ACPNPEVQTD LTIGGIIDY WESN |
-Macromolecule #6: The carbonic anhydrase CsoSCA
Macromolecule | Name: The carbonic anhydrase CsoSCA / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Prochlorococcus (bacteria) |
Sequence | String: MPLRGLAKAK NFTLGPTAPM KTFTENVHSQ NNEINNLKKI DKTHNLTNNS QNEKLYKYES QIKSSFDRI VPTLKEIARI QHHEDFINTA QSISKQNLGI NLPTHILDKS WVKPLDMRAL Y AWCAFKQH EKLSDNFFEN DPLEGSFGSP NANNFETALL DCGIHLLDIT ...String: MPLRGLAKAK NFTLGPTAPM KTFTENVHSQ NNEINNLKKI DKTHNLTNNS QNEKLYKYES QIKSSFDRI VPTLKEIARI QHHEDFINTA QSISKQNLGI NLPTHILDKS WVKPLDMRAL Y AWCAFKQH EKLSDNFFEN DPLEGSFGSP NANNFETALL DCGIHLLDIT PCSDGRLAHS VA YVMRIPF SAVRRRSHAG ALFDIENTVN RWVKTEHKRY RENNPNEAHE DTRYLKIVTY HFS SVDPLH QGCAAHGSDD KLAAKEGSEK LLAFKEAVEN SFCCGASVDL MLIGLDTDTD SLKI HLSSS DGKIDLENTI SSLDIYNSTI NFSKDEAEKE ICQIISGNSN KVQLKGLDKF VYKLI VNNI SQIDYVKKFH KGSYEDIGHA ERFIGVGIGF KEVHLRNLTY FAHLDTVEEG APDLDV GVK IFTGLNVSQD LPIPIVIRFD YSGKVPGAKE RAAKDCYRVN NAISIRYKSL VDKGLLH TC LTIRDRDNIH SAQIIGMSLD QKTKEAH |
-Macromolecule #7: The scaffolding protein CsoS2
Macromolecule | Name: The scaffolding protein CsoS2 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Prochlorococcus (bacteria) |
Sequence | String: MSTKTSREIA LERRKAMSDG GKKAALHSSS TKDRVRSSQD INSTGATSSN KKVLTSPSKS NIPANKIAR KSTSSKLSSK ELGIERRKAM STHGKSAINS SDRTRTDVKS DIKVNKVIST E KPQALKDH NNNIKDNQVV KQNIKRRINQ KRKPITNTSR DIVLARREAQ ...String: MSTKTSREIA LERRKAMSDG GKKAALHSSS TKDRVRSSQD INSTGATSSN KKVLTSPSKS NIPANKIAR KSTSSKLSSK ELGIERRKAM STHGKSAINS SDRTRTDVKS DIKVNKVIST E KPQALKDH NNNIKDNQVV KQNIKRRINQ KRKPITNTSR DIVLARREAQ SKHGKSASKQ NT SAASLAR RGDPDLSSRE ISQRVRELRS KTGSTSKQGN GKCRPCGPNK NGSKLNIADA SWK VGKSET DSGQTVTGTQ ANRSLKTTGN EASTCRTVTG TQYMGAEVTG QFCQDKPKYK QPIR ASVTT TTSGNKVTGN EVGRSEKVTG DEPGTCKNLT GTEYISANQS KKYCGEVIKK PSKVM QSIT TDGLKVSGSL PGRSSLVTGD ESGSGKQLTG DQYLGSEPSP KGKSFEKVGS YDTLNG NNV TGTGVGRSDY VTGNEYGSCK NLTGDEYIGS QQYEKFCGST PKPEARKVGL SLSSKSN LI SGTMTGRSKI VTGDEPGSCK VLTGTPYAGL DQINDNCNAE IADDMKSRAT VNSGNNSN A RLTGLQPGIG GVMTGATKGS CKNLTGTPYI GGDQFLSNCE TPPNDASYAN QEKSASNSW KEFSVNSPSR EKYSAKNTEG VTGNRYEDSS KITGPFDMAE DKVTGTEQFR FEPNKNMTYK QKMKQEESQ NIDIPTDKKE PSKITGEGQS AGNITGDDWD RGDKVTGTEG VSARKRNPSR A GFMGAMPP VDNKRNDETE KPDFLITGSS GNTRDGQLVT FSGGARG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.5 Details: 10 mM Bicine, 1 mM EDTA, 10 mM MgCl2, and dissolved in natural sea water, pH 8.5, supplemented with 0.6 mM PMSF and 20 mM NaHCO3 |
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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 K3 (6k x 4k) / Average electron dose: 1.25 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: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: alphaFold predicted model |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3634 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |