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- EMDB-30499: Cryo-EM structure of bicarbonate transporter SbtA in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-30499
TitleCryo-EM structure of bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB from Synechocystis sp. PCC 6803
Map data
Sample
  • Complex: SbtA-SbtB complex
    • Protein or peptide: Slr1512 protein
    • Protein or peptide: Membrane-associated protein slr1513
  • Ligand: SODIUM ION
  • Ligand: ADENOSINE MONOPHOSPHATE
Keywordsbicarbonate transporter / PII-like signaling protein / 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 substr. Kazusa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsLiu XY / Jiang YL
Funding support China, 2 items
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, 2020-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cyf
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30499.png

Downloads & links

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Map

FileDownload / File: emd_30499.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.035
Minimum - Maximum-0.104490094 - 0.16984968
Average (Standard dev.)0.00036056552 (±0.008184638)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z208.000208.000208.000
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1040.1700.000

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Supplemental data

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Sample components

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Entire : SbtA-SbtB complex

EntireName: SbtA-SbtB complex
Components
  • Complex: SbtA-SbtB complex
    • Protein or peptide: Slr1512 protein
    • Protein or peptide: Membrane-associated protein slr1513
  • Ligand: SODIUM ION
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: SbtA-SbtB complex

SupramoleculeName: SbtA-SbtB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 substr. Kazusa
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Slr1512 protein

MacromoleculeName: Slr1512 protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 substr. Kazusa
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 slr1513

MacromoleculeName: Membrane-associated protein slr1513 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 substr. Kazusa
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 / Details: 25 mM Tris-HCl pH=8.0, 300 mM NaCl, 5% glycerol
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1332746
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 41547
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7cyf:
Cryo-EM structure of bicarbonate transporter SbtA in complex with PII-like signaling protein SbtB from Synechocystis sp. PCC 6803

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