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- PDB-7cyf: Cryo-EM structure of bicarbonate transporter SbtA in complex with... -

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Basic information

Entry
Database: PDB / ID: 7cyf
TitleCryo-EM structure of bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB from Synechocystis sp. PCC 6803
Components
  • Membrane-associated protein slr1513
  • Slr1512 protein
KeywordsTRANSPORT PROTEIN / bicarbonate transporter / PII-like signaling protein
Function / homology
Function and homology information


regulation of nitrogen utilization / plasma membrane-derived thylakoid membrane / enzyme regulator activity / membrane
Similarity search - Function
Na+-dependent bicarbonate transporter superfamily / Na+-dependent bicarbonate transporter superfamily / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Slr1512 protein / Membrane-associated protein slr1513
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 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 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
A: Slr1512 protein
B: Slr1512 protein
C: Slr1512 protein
D: Membrane-associated protein slr1513
E: Membrane-associated protein slr1513
F: Membrane-associated protein slr1513
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,19012
Polymers155,0796
Non-polymers1,1116
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18520 Å2
ΔGint-151 kcal/mol
Surface area48170 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
#2: Protein Membrane-associated protein slr1513 / SbtB


Mass: 12021.810 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: slr1513 / Production host: Escherichia coli (E. coli) / References: UniProt: P73954
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
Has ligand of interestY
Has protein modificationY

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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: SbtA-SbtB complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.15 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 / Details: 25 mM Tris-HCl pH=8.0, 300 mM NaCl, 5% glycerol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
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 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
4CTFFINDCTF correction
10RELIONfinal Euler assignment
12RELION3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1332746
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41547 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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