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Entry
Database: PDB / ID: 4bpq
TitleStructure and substrate induced conformational changes of the secondary citrate-sodium symporter CitS revealed by electron crystallography
ComponentsCITRATE\:SODIUM SYMPORTER
KeywordsTRANSPORT PROTEIN / SECONDARY TRANSPORTER / MEMBRANE PROTEIN
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 6 Å
AuthorsKebbel, F. / Kurz, M. / Arheit, M. / Gruetter, M.G. / Stahlberg, H.
CitationJournal: Structure / Year: 2013
Title: Structure and substrate-induced conformational changes of the secondary citrate/sodium symporter CitS revealed by electron crystallography.
Authors: Fabian Kebbel / Mareike Kurz / Marcel Arheit / Markus G Grütter / Henning Stahlberg /
Abstract: The secondary Na+/citrate symporter CitS of Klebsiella pneumoniae is the best-characterized member of the 2-hydroxycarboxylate transporter family. The recent projection structure gave insight into ...The secondary Na+/citrate symporter CitS of Klebsiella pneumoniae is the best-characterized member of the 2-hydroxycarboxylate transporter family. The recent projection structure gave insight into its overall structural organization. Here, we present the three-dimensional map of dimeric CitS obtained with electron crystallography. Each monomer has 13 a-helical transmembrane segments; six are organized in a distal helix cluster and seven in the central dimer interface domain. Based on structural analyses and comparison to VcINDY, we propose a molecular model for CitS, assign the helices, and demonstrate the internal structural symmetry. We also present projections of CitS in several conformational states induced by the presence and absence of sodium and citrate as substrates. Citrate binding induces a defined movement of a helices within the distal helical cluster. Based on this, we propose a substrate translocation site and conformational changes that are in agreement with the transport model of ‘‘alternating access’’.
History
DepositionMay 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: database_2 / diffrn_radiation ...database_2 / diffrn_radiation / em_image_scans / em_single_particle_entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation.pdbx_scattering_type

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Assembly

Deposited unit
A: CITRATE\:SODIUM SYMPORTER
B: CITRATE\:SODIUM SYMPORTER


Theoretical massNumber of molelcules
Total (without water)54,1622
Polymers54,1622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)1.000, 1.000, 1.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CITRATE\:SODIUM SYMPORTER / CITS


Mass: 27081.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
Sequence detailsTHE SAMPLE SEQUENCE HAS UNIPROT ACCESSION B5Y216. BUT THE REGISTER OF THE RESIDUES ON THE EM VOLUME ...THE SAMPLE SEQUENCE HAS UNIPROT ACCESSION B5Y216. BUT THE REGISTER OF THE RESIDUES ON THE EM VOLUME MAP IS UNKNOWN, HENCE THE MODEL IS BUILT IN AS A POLY-ALA MODEL. THE COORDINATES REPRESENTS THE TRANSMEMBRANE HELICES OF THE CITRATE:SODIUM SYMPORTER

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 79
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: secondary citrate-sodium symporter CitS / Type: COMPLEX
Buffer solutionpH: 4.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Crystal growpH: 4.5 / Details: pH 4.5

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Data collection

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Dec 31, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 6 e/Å2 / Film or detector model: KODAK SO-163 FILM
DiffractionMean temperature: 87 K
DetectorDate: Dec 12, 2012
RadiationScattering type: electron
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 6 Å / Num. obs: 11480 / % possible obs: 79 %

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Processing

Software
NameClassification
2DXmodel building
2DXrefinement
2DXdata scaling
2DXphasing
3D reconstructionResolution: 6 Å / Resolution method: OTHER / Symmetry type: 2D CRYSTAL
RefinementHighest resolution: 6 Å
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 0 0 3110

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