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- PDB-7b4m: CryoEM structure of the human sodium proton exchanger NHA2 in nanodisc -

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Basic information

Entry
Database: PDB / ID: 7b4m
TitleCryoEM structure of the human sodium proton exchanger NHA2 in nanodisc
ComponentsSodium/hydrogen exchanger 9B2
KeywordsMEMBRANE PROTEIN / secondary active transporter / membrane transport / ion antiport / pH regulation
Function / homology
Function and homology information


lithium:proton antiporter activity / lithium ion transport / positive regulation of osteoclast development / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / flagellated sperm motility / clathrin-dependent endocytosis / inorganic cation transmembrane transport ...lithium:proton antiporter activity / lithium ion transport / positive regulation of osteoclast development / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / flagellated sperm motility / clathrin-dependent endocytosis / inorganic cation transmembrane transport / sodium ion transport / mitochondrial membrane / recycling endosome / Stimuli-sensing channels / synaptic vesicle membrane / recycling endosome membrane / monoatomic ion transmembrane transport / basolateral plasma membrane / mitochondrial inner membrane / apical plasma membrane / mitochondrion / identical protein binding / plasma membrane
Similarity search - Function
: / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane
Similarity search - Domain/homology
Sodium/hydrogen exchanger 9B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsWoehlert, D. / Kuhlbrandt, W. / Yildiz, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB807 Germany
CitationJournal: To Be Published
Title: CryoEM structure of the human sodium proton exchanger NHA2 in nanodisc
Authors: Woehlert, D. / Kuhlbrandt, W. / Yildiz, O.
History
DepositionDec 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Sodium/hydrogen exchanger 9B2
B: Sodium/hydrogen exchanger 9B2


Theoretical massNumber of molelcules
Total (without water)115,2232
Polymers115,2232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2220 Å2
ΔGint-16 kcal/mol
Surface area43780 Å2
MethodPISA

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Components

#1: Protein Sodium/hydrogen exchanger 9B2 / Na(+)/H(+) exchanger NHA2 / Na(+)/H(+) exchanger-like domain-containing protein 2 / NHE domain- ...Na(+)/H(+) exchanger NHA2 / Na(+)/H(+) exchanger-like domain-containing protein 2 / NHE domain-containing protein 2 / Sodium/hydrogen exchanger-like domain-containing protein 2 / Solute carrier family 9 subfamily B member 2


Mass: 57611.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9B2, NHA2, NHEDC2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q86UD5

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human sodium proton exchanger NHA2 in nanodisc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1251
Image scansMovie frames/image: 40

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.15.2_3472refinement
PHENIX1.15.2_3472refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 285970
3D reconstructionResolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47284 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00286900
ELECTRON MICROSCOPYf_angle_d0.70619400
ELECTRON MICROSCOPYf_chiral_restr0.03931174
ELECTRON MICROSCOPYf_plane_restr0.00451144
ELECTRON MICROSCOPYf_dihedral_angle_d6.68424026

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