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- PDB-7cye: Cryo-EM structure of sodium-dependent bicarbonate transporter Sbt... -

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Basic information

Entry
Database: PDB / ID: 7cye
TitleCryo-EM structure of sodium-dependent bicarbonate transporter SbtA from Synechocystis sp. PCC 6803
ComponentsSlr1512 protein
KeywordsTRANSPORT PROTEIN / bicarbonate transporter
Function / homologyNa+-dependent bicarbonate transporter superfamily / Na+-dependent bicarbonate transporter superfamily / membrane / Slr1512 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsLiu, X.Y. / Jiang, Y.L. / Wang, L. / Hou, W.T. / Chen, Y. / Zhou, C.Z.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDA24020302, XDB37020301 and XDB37020202 China
National Natural Science Foundation of China (NSFC)31630001 China
CitationJournal: 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
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Slr1512 protein
B: Slr1512 protein
C: Slr1512 protein


Theoretical massNumber of molelcules
Total (without water)119,0143
Polymers119,0143
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5860 Å2
ΔGint-58 kcal/mol
Surface area39050 Å2

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Components

#1: Protein Slr1512 protein / SbtA


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 interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: bicarbonate transporter SbtA / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 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 solutionpH: 8
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1394695
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110385 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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