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- PDB-7s24: Crystal structure of the Na+/H+ antiporter NhaA at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 7s24
TitleCrystal structure of the Na+/H+ antiporter NhaA at pH 6.5
ComponentsNa(+)/H(+) antiporter NhaA
KeywordsTRANSPORT PROTEIN
Function / homologyNa+/H+ antiporter NhaA / Na+/H+ antiporter domain superfamily / Na+/H+ antiporter 1 / sodium:proton antiporter activity / regulation of pH / plasma membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Na(+)/H(+) antiporter NhaA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDrew, D. / Brock, J. / Uzdavinys, P. / Matsuoka, R.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118772 Sweden
CitationJournal: Nat Commun / Year: 2022
Title: Crystal structure of the Na + /H + antiporter NhaA at active pH reveals the mechanistic basis for pH sensing.
Authors: Winkelmann, I. / Uzdavinys, P. / Kenney, I.M. / Brock, J. / Meier, P.F. / Wagner, L.M. / Gabriel, F. / Jung, S. / Matsuoka, R. / von Ballmoos, C. / Beckstein, O. / Drew, D.
History
DepositionSep 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na(+)/H(+) antiporter NhaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2564
Polymers42,3041
Non-polymers9513
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.553, 47.335, 56.392
Angle α, β, γ (deg.)78.002, 67.119, 79.240
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Na(+)/H(+) antiporter NhaA / Sodium/proton antiporter NhaA


Mass: 42304.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nhaA, nahA / Production host: Escherichia coli (E. coli) / References: UniProt: Q53YW7
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1 M MES pH 6.5, 0.1 M NaCl, 0.1 M CaCl2, 24-45 % (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9667 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9667 Å / Relative weight: 1
ReflectionResolution: 2.2→34.84 Å / Num. obs: 20042 / % possible obs: 91.64 % / Redundancy: 3.8 % / Biso Wilson estimate: 39.08 Å2 / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 7.22
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 2006 / CC1/2: 0.531 / CC star: 0.833 / % possible all: 92.91

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AU5

4au5


Resolution: 2.2→34.84 Å / SU ML: 0.2392 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.1019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 1414 7.06 %
Rwork0.209 18628 -
obs0.2109 20042 91.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.87 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 66 58 2923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362921
X-RAY DIFFRACTIONf_angle_d0.62783961
X-RAY DIFFRACTIONf_chiral_restr0.0399487
X-RAY DIFFRACTIONf_plane_restr0.0048473
X-RAY DIFFRACTIONf_dihedral_angle_d14.27381030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.27341400.25221866X-RAY DIFFRACTION92.91
2.28-2.370.27621450.23651898X-RAY DIFFRACTION92.53
2.37-2.480.27981370.22271862X-RAY DIFFRACTION91.61
2.48-2.610.25391420.20641869X-RAY DIFFRACTION91
2.61-2.770.20931340.19171792X-RAY DIFFRACTION88.07
2.77-2.990.27211190.20171624X-RAY DIFFRACTION80.62
2.99-3.290.23251440.20571719X-RAY DIFFRACTION84.87
3.29-3.760.23571490.19812004X-RAY DIFFRACTION98.76
3.76-4.740.24131550.2112017X-RAY DIFFRACTION98.77
4.74-34.840.20481490.20831977X-RAY DIFFRACTION97.61
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1477961171-0.4598365884760.1486852533263.25626238906-0.2432830855182.23520777272-0.0370346647558-0.0491828647687-0.01664305936750.3838943993530.05471327976580.0888489686210.01396408941430.225199029594-0.01119687889590.2252723980990.02444590574030.01973241280660.242198462522-0.002737044812110.29588542353532.0786838814-16.8587197708-16.252227258
21.86267712347-0.439898065845-0.004708200059672.414512933490.02673760696372.23856080615-0.0523352662424-0.2369682014280.04344233034520.2747870374140.05063773971880.02247379834-0.03116941877660.1560958958410.01669207728610.259627577464-0.04114670517570.004196249552360.274321207237-0.01882021287660.40070132114128.1654803678-12.804637605-15.4451850512
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 149 )10 - 1491 - 140
22chain 'A' and (resid 150 through 384 )150 - 384141 - 375

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