+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35202 | |||||||||
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Title | The cryo-EM structure of OsCyc1 tetramer state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | syn-copalyl diphosphate synthase / labdane-related diterpenoids / oligomer cryo-EM structure / plant defense / PLANT PROTEIN / ISOMERASE | |||||||||
Function / homology | Function and homology information syn-copalyl-diphosphate synthase / syn-copalyl diphosphate synthase activity / gibberellin biosynthetic process / terpene synthase activity / chloroplast / defense response / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Ma XL / Xu HF / Tong YR / Luo YF / Dong QH / Jiang T | |||||||||
Funding support | 1 items
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Citation | Journal: Commun Chem / Year: 2023 Title: Structural and functional investigations of syn-copalyl diphosphate synthase from Oryza sativa. Authors: Xiaoli Ma / Haifeng Xu / Yuru Tong / Yunfeng Luo / Qinghua Dong / Tao Jiang / Abstract: The large superfamily of labdane-related diterpenoids is defined by the cyclization of linear geranylgeranyl pyrophosphate (GGPP), catalyzed by copalyl diphosphate synthases (CPSs) to form the basic ...The large superfamily of labdane-related diterpenoids is defined by the cyclization of linear geranylgeranyl pyrophosphate (GGPP), catalyzed by copalyl diphosphate synthases (CPSs) to form the basic decalin core, the copalyl diphosphates (CPPs). Three stereochemically distinct CPPs have been found in plants, namely (+)-CPP, ent-CPP and syn-CPP. Here, we used X-ray crystallography and cryo-EM methods to describe different oligomeric structures of a syn-copalyl diphosphate synthase from Oryza sativa (OsCyc1), and provided a cryo-EM structure of OsCyc1 mutant in complex with the substrate GGPP. Further analysis showed that tetramers are the dominant form of OsCyc1 in solution and are not necessary for enzyme activity in vitro. Through rational design, we identified an OsCyc1 mutant that can generate ent-CPP in addition to syn-CPP. Our work provides a structural and mechanistic basis for comparing different CPSs and paves the way for further enzyme design to obtain diterpene derivatives with specific chirality. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35202.map.gz | 78.2 MB | EMDB map data format | |
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Header (meta data) | emd-35202-v30.xml emd-35202.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_35202.png | 105.6 KB | ||
Filedesc metadata | emd-35202.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35202 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35202 | HTTPS FTP |
-Related structure data
Related structure data | 8i6pMC 8i6tC 8i6uC 8ih5C 8kbwC 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_35202.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : The cryo-EM structure of OsCyc1 tetramer state
Entire | Name: The cryo-EM structure of OsCyc1 tetramer state |
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Components |
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-Supramolecule #1: The cryo-EM structure of OsCyc1 tetramer state
Supramolecule | Name: The cryo-EM structure of OsCyc1 tetramer state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Oryza sativa Japonica Group (Japanese rice) |
Molecular weight | Theoretical: 320 KDa |
-Macromolecule #1: Syn-copalyl diphosphate synthase, chloroplastic
Macromolecule | Name: Syn-copalyl diphosphate synthase, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: syn-copalyl-diphosphate synthase |
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Source (natural) | Organism: Oryza sativa Japonica Group (Japanese rice) |
Molecular weight | Theoretical: 88.427445 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MPVFTASFQC VTLFGQPASA ADAQPLLQGQ RPFLHLHARR RRPCGPMLIS KSPPYPASEE TREWEADGQH EHTDELRETT TTMIDGIRT ALRSIGEGEI SISAYDTSLV ALLKRLDGGD GPQFPSTIDW IVQNQLPDGS WGDASFFMMG DRIMSTLACV V ALKSWNIH ...String: MPVFTASFQC VTLFGQPASA ADAQPLLQGQ RPFLHLHARR RRPCGPMLIS KSPPYPASEE TREWEADGQH EHTDELRETT TTMIDGIRT ALRSIGEGEI SISAYDTSLV ALLKRLDGGD GPQFPSTIDW IVQNQLPDGS WGDASFFMMG DRIMSTLACV V ALKSWNIH TDKCERGLLF IQENMWRLAH EEEDWMLVGF EIALPSLLDM AKDLDLDIPY DEPALKAIYA ERERKLAKIP RD VLHSMPT TLLHSLEGMV DLDWEKLLKL RCLDGSFHCS PASTATAFQQ TGDQKCFEYL DGIVKKFNGG VPCIYPLDVY ERL WAVDRL TRLGISRHFT SEIEDCLDYI FRNWTPDGLA HTKNCPVKDI DDTAMGFRLL RLYGYQVDPC VLKKFEKDGK FFCL HGESN PSSVTPMYNT YRASQLKFPG DDGVLGRAEV FCRSFLQDRR GSNRMKDKWA IAKDIPGEVE YAMDYPWKAS LPRIE TRLY LDQYGGSGDV WIGKVLHRMT LFCNDLYLKA AKADFSNFQK ECRVELNGLR RWYLRSNLEK FGGTDPQTTL MTSYFL ASA NIFEANRAAE RLGWARVALL ADAVSSHFRR IGGPKNSTSN LEELISLVPF DDAYSGSLRE AWKQWLMAWT AKESSQE SI EGDTAILLVR AIEIFGGRHV LTGQRPDLWE YSQLEQLTSS ICCKLSRRVL AQENGESTEK VEEIDQQVDL EMQELTRR V LQGCSAINRL TRETFLHVVK SFCYVAYCSP ETIDSHIDKV IFQDVIEFHH HHHH UniProtKB: Syn-copalyl diphosphate synthase, chloroplastic |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.8 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
Details: (20 mM Tris-HCl pH 8.0, 200 mM NaCl, 2 mM DTT, 5 mM MgCl2 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | R 1.2/1.3 Au 300 mesh holey carbon films (Quantifoil Micro Tools) |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 149837 |