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Yorodumi- EMDB-30499: Cryo-EM structure of bicarbonate transporter SbtA in complex with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30499 | |||||||||
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Title | Cryo-EM structure of bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB from Synechocystis sp. PCC 6803 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Na+-dependent bicarbonate transporter superfamily / Na+-dependent bicarbonate transporter superfamily / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / plasma membrane-derived thylakoid membrane / membrane / Slr1512 protein / Membrane-associated protein slr1513 Function and homology information | |||||||||
Biological species | Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
Authors | Liu XY / Jiang YL / Wang L / Hou WT / Chen Y / Zhou CZ | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Discov / Year: 2021 Title: Structures of cyanobacterial bicarbonate transporter SbtA and its complex with PII-like SbtB. Authors: Xiao-Yu Liu / Wen-Tao Hou / Liang Wang / Bo Li / Yu Chen / Yuxing Chen / Yong-Liang Jiang / Cong-Zhao Zhou / | |||||||||
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_30499.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-30499-v30.xml emd-30499.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_30499.png | 225.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30499 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30499 | HTTPS FTP |
-Validation report
Summary document | emd_30499_validation.pdf.gz | 504.6 KB | Display | EMDB validaton report |
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Full document | emd_30499_full_validation.pdf.gz | 504.1 KB | Display | |
Data in XML | emd_30499_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_30499_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30499 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30499 | HTTPS FTP |
-Related structure data
Related structure data | 7cyfMC 7cyeC 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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-Map
File | Download / File: emd_30499.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SbtA-SbtB complex
Entire | Name: SbtA-SbtB complex |
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Components |
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-Supramolecule #1: SbtA-SbtB complex
Supramolecule | Name: SbtA-SbtB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 substr. Kazusa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Slr1512 protein
Macromolecule | Name: Slr1512 protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 substr. Kazusa |
Molecular weight | Theoretical: 39.671246 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDFLSNFLTD FVGQLQSPTL AFLIGGMVIA ALGTQLVIPE AISTIIVFML LTKIGLTGGM AIRNSNLTEM LLPVAFSVIL GILIVFIAR FTLAKLPNVR TVDALATGGL FGAVSGSTMA AALTTLEESK ISYEAWAGAL YPFMDIPALV TAIVVANIYL N KRKRKSAA ...String: MDFLSNFLTD FVGQLQSPTL AFLIGGMVIA ALGTQLVIPE AISTIIVFML LTKIGLTGGM AIRNSNLTEM LLPVAFSVIL GILIVFIAR FTLAKLPNVR TVDALATGGL FGAVSGSTMA AALTTLEESK ISYEAWAGAL YPFMDIPALV TAIVVANIYL N KRKRKSAA ASIEESFSKQ PVAAGDYGDQ TDYPRTRQEY LSQQEPEDNR VKIWPIIEES LQGPALSAML LGLALGIFTK PE SVYEGFY DPLFRGLLSI LMLIMGMEAW SRIGELRKVA QWYVVYSLIA PIVHGFIAFG LGMIAHYATG FSLGGVVVLA VIA ASSSDI SGPPTLRAGI PSANPSAYIG SSTAIGTPIA IGVCIPLFIG LAQTLGAG |
-Macromolecule #2: Membrane-associated protein slr1513
Macromolecule | Name: Membrane-associated protein slr1513 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 substr. Kazusa |
Molecular weight | Theoretical: 12.02181 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAKPANKLVI VTEKILLKKI AKIIDESGAK GYTVMNTGGK GSRNVRSSGQ PNTSDIEANI KFEILTETRE MAEEIADRVA VKYFNDYAG IIYICSAEVL YGHTFCGPEG C |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 3 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #4: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ChemComp-AMP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 25 mM Tris-HCl pH=8.0, 300 mM NaCl, 5% glycerol |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7cyf: |