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- PDB-8zor: Cryo-EM structure of bicarbonate transporter SbtA in complex with... -

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Basic information

Entry
Database: PDB / ID: 8zor
TitleCryo-EM structure of bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB (T-loop truncation) from Synechocystis sp. PCC 6803
Components
  • Membrane-associated protein slr1513
  • Slr1512 protein
KeywordsTRANSPORT PROTEIN / Complex / T-loop truncation
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
BICARBONATE ION / 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: 3.1 Å
AuthorsHou, W.T. / Zhou, C.Z.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020301 China
Chinese Academy of SciencesXDA24020302 China
CitationJournal: To Be Published
Title: Cryo-EM structure of bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB T-loop truncation from Synechocystis sp. PCC 6803
Authors: Hou, W.T. / Zhou, C.Z.
History
DepositionMay 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Slr1512 protein
D: Membrane-associated protein slr1513
C: Slr1512 protein
E: Membrane-associated protein slr1513
G: Slr1512 protein
H: Membrane-associated protein slr1513
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,2629
Polymers155,0796
Non-polymers1833
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Slr1512 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 / Kazusa / Gene: slr1512 / Production host: Escherichia coli (E. coli) / References: UniProt: P73953
#2: Protein Membrane-associated protein slr1513


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 / Kazusa / Gene: slr1513 / Production host: Escherichia coli (E. coli) / References: UniProt: P73954
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
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: Bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB (T-loop truncation)
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Synechocystis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: SPOT SCAN
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
4cryoSPARCCTF correction
8PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178612 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039594
ELECTRON MICROSCOPYf_angle_d0.51813032
ELECTRON MICROSCOPYf_dihedral_angle_d3.4241323
ELECTRON MICROSCOPYf_chiral_restr0.0411593
ELECTRON MICROSCOPYf_plane_restr0.0041599

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