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- EMDB-31135: Bicarbonate transporter complex SbtA-SbtB bound to AMP -

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Basic information

Entry
Database: EMDB / ID: EMD-31135
TitleBicarbonate transporter complex SbtA-SbtB bound to AMP
Map data
Sample
  • Complex: Bicarbonate transporter SbtA in complex with regulator SbtB
    • Protein or peptide: Sodium-dependent bicarbonate transporter SbtA
    • Protein or peptide: Membrane-associated protein SbtB
  • Ligand: SODIUM ION
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsBicarbonate transporter / CO2 concentrating mechanism / Allosteric inhibition / Photosynthesis / TRANSPORT 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
Slr1512 protein / Membrane-associated protein slr1513
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria) / Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFang S / Huang X
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Molecular mechanism underlying transport and allosteric inhibition of bicarbonate transporter SbtA.
Authors: Sunzhenhe Fang / Xiaowei Huang / Xue Zhang / Minhua Zhang / Yahui Hao / Hui Guo / Lu-Ning Liu / Fang Yu / Peng Zhang /
Abstract: SbtA is a high-affinity, sodium-dependent bicarbonate transporter found in the cyanobacterial CO-concentrating mechanism (CCM). SbtA forms a complex with SbtB, while SbtB allosterically regulates the ...SbtA is a high-affinity, sodium-dependent bicarbonate transporter found in the cyanobacterial CO-concentrating mechanism (CCM). SbtA forms a complex with SbtB, while SbtB allosterically regulates the transport activity of SbtA by binding with adenyl nucleotides. The underlying mechanism of transport and regulation of SbtA is largely unknown. In this study, we report the three-dimensional structures of the cyanobacterial sp. PCC 6803 SbtA-SbtB complex in both the presence and absence of HCO and/or AMP at 2.7 Å and 3.2 Å resolution. An analysis of the inward-facing state of the SbtA structure reveals the HCO/Na binding site, providing evidence for the functional unit as a trimer. A structural comparison found that SbtA adopts an elevator mechanism for bicarbonate transport. A structure-based analysis revealed that the allosteric inhibition of SbtA by SbtB occurs mainly through the T-loop of SbtB, which binds to both the core domain and the scaffold domain of SbtA and locks it in an inward-facing state. T-loop conformation is stabilized by the AMP molecules binding at the SbtB trimer interfaces and may be adjusted by other adenyl nucleotides. The unique regulatory mechanism of SbtA by SbtB makes it important to study inorganic carbon uptake systems in CCM, which can be used to modify photosynthesis in crops.
History
DepositionMar 24, 2021-
Header (metadata) releaseMay 26, 2021-
Map releaseMay 26, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-7egk
  • Surface level: 0.05
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31135.png

Downloads & links

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Map

FileDownload / File: emd_31135.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 258.552 Å		1.08 Å/pix.
x 240 pix.
= 258.552 Å		1.08 Å/pix.
x 240 pix.
= 258.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.09080606 - 0.17949589
Average (Standard dev.)0.00027114412 (±0.0043422845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 258.552 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.07731.07731.0773
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z258.552258.552258.552
α/β/γ90.00090.00090.000
start NX/NY/NZ1229869
NX/NY/NZ377377377
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0910.1790.000

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Supplemental data

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Half map: #1

Fileemd_31135_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_31135_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Bicarbonate transporter SbtA in complex with regulator SbtB

EntireName: Bicarbonate transporter SbtA in complex with regulator SbtB
Components
  • Complex: Bicarbonate transporter SbtA in complex with regulator SbtB
    • Protein or peptide: Sodium-dependent bicarbonate transporter SbtA
    • Protein or peptide: Membrane-associated protein SbtB
  • Ligand: SODIUM ION
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: Bicarbonate transporter SbtA in complex with regulator SbtB

SupramoleculeName: Bicarbonate transporter SbtA in complex with regulator SbtB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Macromolecule #1: Sodium-dependent bicarbonate transporter SbtA

MacromoleculeName: Sodium-dependent bicarbonate transporter SbtA / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Molecular weightTheoretical: 39.671246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: Slr1512 protein

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Macromolecule #2: Membrane-associated protein SbtB

MacromoleculeName: Membrane-associated protein SbtB / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Molecular weightTheoretical: 12.02181 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKPANKLVI VTEKILLKKI AKIIDESGAK GYTVMNTGGK GSRNVRSSGQ PNTSDIEANI KFEILTETRE MAEEIADRVA VKYFNDYAG IIYICSAEVL YGHTFCGPEG C

UniProtKB: Membrane-associated protein slr1513

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125998
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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