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- PDB-4czb: Structure of the sodium proton antiporter MjNhaP1 from Methanocal... -

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Basic information

Entry
Database: PDB / ID: 4czb
TitleStructure of the sodium proton antiporter MjNhaP1 from Methanocaldococcus jannaschii at pH 8.
Components(NA(+)/H(+) ANTIPORTER 1) x 2
KeywordsMEMBRANE PROTEIN / ANTIPORTER / TRANSPORTER / EXCHANGER / CPA
Function / homology
Function and homology information


potassium:proton antiporter activity / sodium ion transport / intracellular potassium ion homeostasis / identical protein binding / plasma membrane
Similarity search - Function
Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane
Similarity search - Domain/homology
: / Na(+)/H(+) antiporter 1
Similarity search - Component
Biological speciesMETHANOCALDOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWoehlert, D. / Paulino, C. / Kapotova, E. / Kuhlbrandt, W. / Yildiz, O.
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 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NA(+)/H(+) ANTIPORTER 1
B: NA(+)/H(+) ANTIPORTER 1
C: NA(+)/H(+) ANTIPORTER 1
D: NA(+)/H(+) ANTIPORTER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,2517
Polymers184,0104
Non-polymers2413
Water00
1
A: NA(+)/H(+) ANTIPORTER 1
B: NA(+)/H(+) ANTIPORTER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2004
Polymers91,9982
Non-polymers2022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-43 kcal/mol
Surface area41550 Å2
MethodPQS
2
C: NA(+)/H(+) ANTIPORTER 1
D: NA(+)/H(+) ANTIPORTER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0513
Polymers92,0122
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-79 kcal/mol
Surface area41560 Å2
MethodPQS
Unit cell
Length a, b, c (Å)98.437, 102.544, 132.096
Angle α, β, γ (deg.)90.00, 105.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 45998.891 Da / Num. of mol.: 3 / Fragment: TRANSPORTER DOMAIN, RESIDUES 1-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60362
#2: Protein NA(+)/H(+) ANTIPORTER 1 / MJNHAP1 / MJNHAP1 ANTIPORTER


Mass: 46012.918 Da / Num. of mol.: 1 / Fragment: TRANSPORTER DOMAIN, RESIDUES 1-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60362
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 8.2 / Details: pH 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763
DetectorDate: Jul 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.5→32 Å / Num. obs: 58249 / % possible obs: 99.3 % / Observed criterion σ(I): 1.7 / Redundancy: 7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 3.5→3.72 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CZ8

4cz8


Resolution: 3.5→32 Å / σ(F): 6
RfactorNum. reflection% reflection
Rfree0.302 3115 -
Rwork0.252 --
obs-58249 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12535 0 13 0 12548

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