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- EMDB-23326: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23326 | |||||||||
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Title | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg) | |||||||||
![]() | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) map | |||||||||
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Function / homology | ![]() cyanophycin synthase (L-aspartate-adding) / cyanophycin synthase (L-arginine-adding) / cyanophycin synthetase activity (L-aspartate-adding) / cyanophycin synthetase activity (L-arginine-adding) / macromolecule biosynthetic process / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
![]() | Sharon I / Grogg M / Hilvert D / Schmeing TM | |||||||||
![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 483.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.7 KB | Display | ![]() |
Images | ![]() | 211.8 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Others | ![]() ![]() | 474.5 MB 474.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 496.4 KB | Display | ![]() |
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Full document | ![]() | 496 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7txuM ![]() 7lg5C ![]() 7lgjC ![]() 7lgmC ![]() 7lgnC ![]() 7lgqC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Projections & Slices |
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Density Histograms |
-Half map: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with...
File | emd_23326_half_map_1.map | ||||||||||||
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Annotation | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with...
File | emd_23326_half_map_2.map | ||||||||||||
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Annotation | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP...
Entire | Name: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg) |
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Components |
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-Supramolecule #1: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP...
Supramolecule | Name: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP...
Macromolecule | Name: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg) type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: MKILKTLTLR GPNYWSIRRK KLIVMRLDLE DLAERPSNSI PGFYEGLIKV LPSLVEHFCS PGYQGGFLER VKEGTYMGHI VEHVALELQE LVGMTAGFGR TRETSTPGV YNVVYEYVDE QAGRYAGRAA VRLCRSLVDT GDYPRLELEK DLEDLRDLGA NSALGPSTET ...String: MKILKTLTLR GPNYWSIRRK KLIVMRLDLE DLAERPSNSI PGFYEGLIKV LPSLVEHFCS PGYQGGFLER VKEGTYMGHI VEHVALELQE LVGMTAGFGR TRETSTPGV YNVVYEYVDE QAGRYAGRAA VRLCRSLVDT GDYPRLELEK DLEDLRDLGA NSALGPSTET IVTEAEARKI PWMLLSARAM VQLGYGVYQQ R IQATLSSH SGILGVELAC DKEGTKTILQ DAGIPVPRGT TIQYFDDLEE AINDVGGYPV VIKPLDGNHG RGITINVRHW QEAIAAYDLA AEESKSRAII VE RYYEGSD HRVLVVNGKL VAVAERIPAH VTGDGSSTIS ELIEKTNQDP NRGDGHDNIL TKIVVNKTAI DVMERQGYNL DSVLPKDEVV YLRATANLST GGI AIDRTD DIHPENIWLM ERVAKVIGLD IAGIDVVTSD ISKPLRETNG VIVEVNAAPG FRMHVAPSQG LPRNVAAPVL DMLFPPGTPS RIPILAVTGT NGKT TTTRL LAHIYRQTGK TVGYTSTDAI YINEYCVEKG DNTGPQSAGV ILRDPTVEVA VLETARGGIL RAGLAFDSCD VGVVLNVAAD HLGLGDIDTI EQMAK VKSV IAEVVDPSGY AVLNADDPLV AAMADKVKAK VAYFSMNPDN PIIQAHVRRN GIAAVYESGY LSILEGSWTL RVEQAKLIPM TMGGMAPFMI ANALAA CLA AFVNGLDVEV IRQGVRTFTT SAEQTPGRMN LFNLGQHHAL VDYAHNPAGY RAVGDFVKNW QGQRFGVVGG PGDRRDSDLI ELGQIAAQVF DRIIVKE DD DKRGRSEGET ADLIVKGILQ ENPGASYEVI LDETIALNKA LDQVEEKGLV VVFPESVTRA IDLIKVRNPI GENLYFQ |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 8 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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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: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |