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- PDB-7b4l: CryoEM structure of the human sodium proton exchanger NHA2 -

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Basic information

Entry
Database: PDB / ID: 7b4l
TitleCryoEM structure of the human sodium proton exchanger NHA2
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 / : / positive regulation of osteoclast development / sperm principal piece / flagellated sperm motility / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / sodium ion transport / monoatomic ion transmembrane transport ...lithium:proton antiporter activity / : / positive regulation of osteoclast development / sperm principal piece / flagellated sperm motility / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / sodium ion transport / monoatomic ion transmembrane transport / mitochondrial membrane / Stimuli-sensing channels / synaptic vesicle membrane / basolateral plasma membrane / mitochondrial inner membrane / endosome membrane / apical plasma membrane / identical protein binding / plasma membrane
Similarity search - Function
Sodium/hydrogen exchanger 9B2 / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family
Similarity search - Domain/homology
TETRADECANE / Chem-POV / UNDECANE / Sodium/hydrogen exchanger 9B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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
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

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,06324
Polymers115,2232
Non-polymers5,84022
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area13260 Å2
ΔGint-42 kcal/mol
Surface area35920 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLUN1 - 443
d_12ens_1NANAO
d_13ens_1POVPOVP
d_14ens_1POVPOVQ
d_15ens_1C14C14R
d_16ens_1C14C14S
d_17ens_1C14C14T
d_18ens_1UNDUNDU
d_19ens_1UNDUNDV
d_110ens_1UNDUNDW
d_111ens_1UNDUNDX
d_112ens_1UNDUNDY
d_21ens_1PROGLUA1 - 443
d_22ens_1NANAB
d_23ens_1POVPOVC
d_24ens_1POVPOVD
d_25ens_1C14C14E
d_26ens_1C14C14F
d_27ens_1C14C14G
d_28ens_1UNDUNDH
d_29ens_1UNDUNDI
d_210ens_1UNDUNDJ
d_211ens_1UNDUNDK
d_212ens_1UNDUNDL

NCS oper: (Code: givenMatrix: (-0.999999999982, 5.59715458854E-6, 1.92899463423E-6), (-5.59715564979E-6, -0.999999999984, -5.5014751263E-7), (1.92899155494E-6, -5.50158309504E-7, 0.999999999998) ...NCS oper: (Code: given
Matrix: (-0.999999999982, 5.59715458854E-6, 1.92899463423E-6), (-5.59715564979E-6, -0.999999999984, -5.5014751263E-7), (1.92899155494E-6, -5.50158309504E-7, 0.999999999998)
Vector: 96.5695181285, 92.2782140751, -3.16066012402E-5)

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Components

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Protein , 1 types, 2 molecules AB

#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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Non-polymers , 5 types, 48 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC / POPC


Mass: 760.076 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#4: Chemical
ChemComp-C14 / TETRADECANE / Tetradecane


Mass: 198.388 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H30
#5: Chemical
ChemComp-UND / UNDECANE / LIPID FRAGMENT / Undecane


Mass: 156.308 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C11H24
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 / Type: COMPLEX / Entity ID: #1 / 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 FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4326

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2243669
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165793 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 57.82 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00257122
ELECTRON MICROSCOPYf_angle_d0.53499572
ELECTRON MICROSCOPYf_chiral_restr0.03811146
ELECTRON MICROSCOPYf_plane_restr0.0051122
ELECTRON MICROSCOPYf_dihedral_angle_d21.41751212
Refine LS restraints NCSType: NCS constraints / Rms dev position: 0.000383998782733 Å

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