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- PDB-4d0a: 3D EM map of the sodium proton antiporter MjNhaP1 from Methanocal... -

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Entry
Database: PDB / ID: 4d0a
Title3D EM map of the sodium proton antiporter MjNhaP1 from Methanocaldococcus jannaschii
ComponentsNA(+)/H(+) ANTIPORTER 1
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / ANTIPORTER / TRANSPORTER / EXCHANGER / CPA
Function / homologySodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / antiporter activity / sodium ion transport / proton transmembrane transport / identical protein binding / plasma membrane / Na(+)/H(+) antiporter 1
Function and homology information
Biological speciesMETHANOCALDOCOCCUS JANNASCHII DSM 2661 (archaea)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 6 Å
AuthorsPaulino, C. / Woehlert, D. / Yildiz, O. / Kuhlbrandt, W.
CitationJournal: Elife / Year: 2014
Title: Structure and transport mechanism of the sodium/proton antiporter MjNhaP1.
Authors: Cristina Paulino / David Wöhlert / Ekaterina Kapotova / Özkan Yildiz / Werner Kühlbrandt /
Abstract: Sodium/proton antiporters are essential for sodium and pH homeostasis and play a major role in human health and disease. We determined the structures of the archaeal sodium/proton antiporter MjNhaP1 ...Sodium/proton antiporters are essential for sodium and pH homeostasis and play a major role in human health and disease. We determined the structures of the archaeal sodium/proton antiporter MjNhaP1 in two complementary states. The inward-open state was obtained by x-ray crystallography in the presence of sodium at pH 8, where the transporter is highly active. The outward-open state was obtained by electron crystallography without sodium at pH 4, where MjNhaP1 is inactive. Comparison of both structures reveals a 7° tilt of the 6 helix bundle. (22)Na(+) uptake measurements indicate non-cooperative transport with an activity maximum at pH 7.5. We conclude that binding of a Na(+) ion from the outside induces helix movements that close the extracellular cavity, open the cytoplasmic funnel, and result in a ∼5 Å vertical relocation of the ion binding site to release the substrate ion into the cytoplasm.
History
DepositionApr 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation / em_image_scans / em_single_particle_entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation.pdbx_scattering_type

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Structure visualization

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Assembly

Deposited unit
B: NA(+)/H(+) ANTIPORTER 1


Theoretical massNumber of molelcules
Total (without water)45,9991
Polymers45,9991
Non-polymers00
Water0
1
B: NA(+)/H(+) ANTIPORTER 1

B: NA(+)/H(+) ANTIPORTER 1


Theoretical massNumber of molelcules
Total (without water)91,9982
Polymers91,9982
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4290 Å2
ΔGint-47.8 kcal/mol
Surface area39960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.500, 103.300, 200.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NA(+)/H(+) ANTIPORTER 1 / MJNHAP1


Mass: 45998.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII DSM 2661 (archaea)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60362

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: sodium proton antiporter MjNhaP1 from Methanocaldococcus jannaschii
Type: COMPLEX
Buffer solutionpH: 4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN
Crystal growpH: 4 / Details: pH 4.0

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Data collection

MicroscopyModel: JEOL KYOTO-3000SFF / Date: Dec 1, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: OTHER / Nominal magnification: 60000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 120 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
DiffractionMean temperature: 4 K
DetectorDate: Dec 1, 2012
RadiationScattering type: electron
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: 2DX / Classification: refinement
3D reconstructionResolution: 6 Å / Resolution method: OTHER / Symmetry type: 2D CRYSTAL
RefinementStarting model: 4CZB

4czb


Highest resolution: 6 Å
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 0 0 3175

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