+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23311 | |||||||||
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Title | Synechocystis sp. UTEX2470 Cyanophycin synthetase 1 with ATP | |||||||||
Map data | Synechocystis sp. UTEX2470 CphA1 with ATP | |||||||||
Sample |
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Keywords | cyanophycin / CphA1 / ATP grasp / ligase | |||||||||
Function / homology | Function and homology information cyanophycin synthase (L-aspartate-adding) / cyanophycin synthase (L-arginine-adding) / cyanophycin synthetase activity (L-aspartate-adding) / cyanophycin synthetase activity (L-arginine-adding) / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6714 (bacteria) / Synechocystis sp. (strain PCC 6714) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.63 Å | |||||||||
Authors | Sharon I / Schmeing TM | |||||||||
Citation | Journal: Nat Chem Biol / Year: 2021 Title: Structures and function of the amino acid polymerase cyanophycin synthetase. Authors: Itai Sharon / Asfarul S Haque / Marcel Grogg / Indrajit Lahiri / Dieter Seebach / Andres E Leschziner / Donald Hilvert / T Martin Schmeing / Abstract: Cyanophycin is a natural biopolymer produced by a wide range of bacteria, consisting of a chain of poly-L-Asp residues with L-Arg residues attached to the β-carboxylate sidechains by isopeptide ...Cyanophycin is a natural biopolymer produced by a wide range of bacteria, consisting of a chain of poly-L-Asp residues with L-Arg residues attached to the β-carboxylate sidechains by isopeptide bonds. Cyanophycin is synthesized from ATP, aspartic acid and arginine by a homooligomeric enzyme called cyanophycin synthetase (CphA1). CphA1 has domains that are homologous to glutathione synthetases and muramyl ligases, but no other structural information has been available. Here, we present cryo-electron microscopy and X-ray crystallography structures of cyanophycin synthetases from three different bacteria, including cocomplex structures of CphA1 with ATP and cyanophycin polymer analogs at 2.6 Å resolution. These structures reveal two distinct tetrameric architectures, show the configuration of active sites and polymer-binding regions, indicate dynamic conformational changes and afford insight into catalytic mechanism. Accompanying biochemical interrogation of substrate binding sites, catalytic centers and oligomerization interfaces combine with the structures to provide a holistic understanding of cyanophycin biosynthesis. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23311.map.gz | 122.5 MB | EMDB map data format | |
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Header (meta data) | emd-23311-v30.xml emd-23311.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23311_fsc.xml | 13.9 KB | Display | FSC data file |
Images | emd_23311.png | 138.7 KB | ||
Masks | emd_23311_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-23311.cif.gz | 5.8 KB | ||
Others | emd_23311_half_map_1.map.gz emd_23311_half_map_2.map.gz | 226.4 MB 226.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23311 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23311 | HTTPS FTP |
-Validation report
Summary document | emd_23311_validation.pdf.gz | 945.3 KB | Display | EMDB validaton report |
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Full document | emd_23311_full_validation.pdf.gz | 944.8 KB | Display | |
Data in XML | emd_23311_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | emd_23311_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23311 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23311 | HTTPS FTP |
-Related structure data
Related structure data | 7lg5MC 7lgjC 7lgmC 7lgnC 7lgqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23311.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Synechocystis sp. UTEX2470 CphA1 with ATP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.855 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23311_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Synechocystis sp. UTEX2470 CphA1 with ATP half map A
File | emd_23311_half_map_1.map | ||||||||||||
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Annotation | Synechocystis sp. UTEX2470 CphA1 with ATP half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Synechocystis sp. UTEX2470 CphA1 with ATP half map B
File | emd_23311_half_map_2.map | ||||||||||||
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Annotation | Synechocystis sp. UTEX2470 CphA1 with ATP half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cyanophycin synthetase 1 with Atp
Entire | Name: Cyanophycin synthetase 1 with Atp |
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Components |
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-Supramolecule #1: Cyanophycin synthetase 1 with Atp
Supramolecule | Name: Cyanophycin synthetase 1 with Atp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Synechocystis sp. PCC 6714 (bacteria) |
-Macromolecule #1: Cyanophycin synthase
Macromolecule | Name: Cyanophycin synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: cyanophycin synthase (L-aspartate-adding) |
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Source (natural) | Organism: Synechocystis sp. (strain PCC 6714) (bacteria) / Strain: PCC 6714 |
Molecular weight | Theoretical: 95.758836 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKILKTLTLR GPNYWSIRRK KLIVMRLDLE DLAERPSNSI PGFYEGLIKV LPSLVEHFCS PGYQGGFLER VKEGTYMGHI VEHVALELQ ELVGMTAGFG RTRETSTPGV YNVVYEYVDE QAGRYAGRAA VRLCRSLVDT GDYPRLELEK DLEDLRDLGA N SALGPSTE ...String: MKILKTLTLR GPNYWSIRRK KLIVMRLDLE DLAERPSNSI PGFYEGLIKV LPSLVEHFCS PGYQGGFLER VKEGTYMGHI VEHVALELQ ELVGMTAGFG RTRETSTPGV YNVVYEYVDE QAGRYAGRAA VRLCRSLVDT GDYPRLELEK DLEDLRDLGA N SALGPSTE TIVTEAEARK IPWMLLSARA MVQLGYGVYQ QRIQATLSSH SGILGVELAC DKEGTKTILQ DAGIPVPRGT TI QYFDDLE EAINDVGGYP VVIKPLDGNH GRGITINVRH WQEAIAAYDL AAEESKSRAI IVERYYEGSD HRVLVVNGKL VAV AERIPA HVTGDGSSTI SELIEKTNQD PNRGDGHDNI LTKIVVNKTA IDVMERQGYN LDSVLPKDEV VYLRATANLS TGGI AIDRT DDIHPENIWL MERVAKVIGL DIAGIDVVTS DISKPLRETN GVIVEVNAAP GFRMHVAPSQ GLPRNVAAPV LDMLF PPGT PSRIPILAVT GTNGKTTTTR LLAHIYRQTG KTVGYTSTDA IYINEYCVEK GDNTGPQSAG VILRDPTVEV AVLETA RGG ILRAGLAFDS CDVGVVLNVA ADHLGLGDID TIEQMAKVKS VIAEVVDPSG YAVLNADDPL VAAMADKVKA KVAYFSM NP DNPIIQAHVR RNGIAAVYES GYLSILEGSW TLRVEQAKLI PMTMGGMAPF MIANALAACL AAFVNGLDVE VIRQGVRT F TTSAEQTPGR MNLFNLGQHH ALVDYAHNPA GYRAVGDFVK NWQGQRFGVV GGPGDRRDSD LIELGQIAAQ VFDRIIVKE DDDKRGRSEG ETADLIVKGI LQENPGASYE VILDETIALN KALDQVEEKG LVVVFPESVT RAIDLIKVRN PIGENLYFQ UniProtKB: Cyanophycin synthetase |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 8 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |