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Yorodumi- PDB-7cye: Cryo-EM structure of sodium-dependent bicarbonate transporter Sbt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cye | |||||||||
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Title | Cryo-EM structure of sodium-dependent bicarbonate transporter SbtA from Synechocystis sp. PCC 6803 | |||||||||
Components | Slr1512 protein | |||||||||
Keywords | TRANSPORT PROTEIN / bicarbonate transporter | |||||||||
Function / homology | Na+-dependent bicarbonate transporter superfamily / Na+-dependent bicarbonate transporter superfamily / membrane / Slr1512 protein Function and homology information | |||||||||
Biological species | Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å | |||||||||
Authors | Liu, X.Y. / Jiang, Y.L. / Wang, L. / Hou, W.T. / Chen, Y. / Zhou, C.Z. | |||||||||
Funding support | China, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7cye.cif.gz | 166.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cye.ent.gz | 133.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cye_validation.pdf.gz | 909.3 KB | Display | wwPDB validaton report |
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Full document | 7cye_full_validation.pdf.gz | 915.9 KB | Display | |
Data in XML | 7cye_validation.xml.gz | 30 KB | Display | |
Data in CIF | 7cye_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/7cye ftp://data.pdbj.org/pub/pdb/validation_reports/cy/7cye | HTTPS FTP |
-Related structure data
Related structure data | 30498MC 7cyfC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 39671.246 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 substr. Kazusa / Gene: slr1512 / Production host: Escherichia coli (E. coli) / References: UniProt: P73953 Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: bicarbonate transporter SbtA / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.12 MDa / Experimental value: NO |
Source (natural) | Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 substr. Kazusa |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||
Particle selection | Num. of particles selected: 1394695 | ||||||||||||||||||
3D reconstruction | Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110385 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL |