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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12002 | |||||||||
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Title | CryoEM structure of the human sodium proton exchanger NHA2 | |||||||||
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![]() | secondary active transporter / membrane transport / ion antiport / pH regulation / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() lithium:proton antiporter activity / lithium ion transport / positive regulation of osteoclast development / sperm principal piece / sodium ion homeostasis / flagellated sperm motility / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / 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 / flagellated sperm motility / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / inorganic cation transmembrane transport / sodium ion transport / monoatomic ion transmembrane transport / mitochondrial membrane / Stimuli-sensing channels / recycling endosome / synaptic vesicle membrane / recycling endosome membrane / basolateral plasma membrane / mitochondrial inner membrane / apical plasma membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Woehlert D / Kuhlbrandt W | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CryoEM structure of the human sodium proton exchanger NHA2 Authors: Woehlert D / Kuhlbrandt W / Yildiz O | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 77.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.2 KB 15.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.8 KB | Display | ![]() |
Images | ![]() | 42.4 KB | ||
Masks | ![]() | 83.7 MB | ![]() | |
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 77.6 MB 77.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b4lMC ![]() 7b4mC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.073 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12002_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12002_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Human sodium proton exchanger NHA2
Entire | Name: Human sodium proton exchanger NHA2 |
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Components |
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-Supramolecule #1: Human sodium proton exchanger NHA2
Supramolecule | Name: Human sodium proton exchanger NHA2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Sodium/hydrogen exchanger 9B2
Macromolecule | Name: Sodium/hydrogen exchanger 9B2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 57.611672 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGDEDKRITY EDSEPSTGMN YTPSMHQEAQ EETVMKLKGI DANEPTEGSI LLKSSEKKLQ ETPTEANHVQ RLRQMLACPP HGLLDRVIT NVTIIVLLWA VVWSITGSEC LPGGNLFGII ILFYCAIIGG KLLGLIKLPT LPPLPSLLGM LLAGFLIRNI P VINDNVQI ...String: MGDEDKRITY EDSEPSTGMN YTPSMHQEAQ EETVMKLKGI DANEPTEGSI LLKSSEKKLQ ETPTEANHVQ RLRQMLACPP HGLLDRVIT NVTIIVLLWA VVWSITGSEC LPGGNLFGII ILFYCAIIGG KLLGLIKLPT LPPLPSLLGM LLAGFLIRNI P VINDNVQI KHKWSSSLRS IALSIILVRA GLGLDSKALK KLKGVCVRLS MGPCIVEACT SALLAHYLLG LPWQWGFILG FV LGAVSPA VVVPSMLLLQ GGGYGVEKGV PTLLMAAGSF DDILAITGFN TCLGIAFSTG STVFNVLRGV LEVVIGVATG SVL GFFIQY FPSRDQDKLV CKRTFLVLGL SVLAVFSSVH FGFPGSGGLC TLVMAFLAGM GWTSEKAEVE KIIAVAWDIF QPLL FGLIG AEVSIASLRP ETVGLCVATV GIAVLIRILT TFLMVCFAGF NLKEKIFISF AWLPKATVQA AIGSVALDTA RSHGE KQLE DYGMDVLTVA FLSILITAPI GSLLIGLLGP RLLQKVEHQN KDEEVQGETS VQV UniProtKB: Sodium/hydrogen exchanger 9B2 |
-Macromolecule #2: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 2 / Number of copies: 2 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 3 / Number of copies: 4 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ![]() ChemComp-POV: |
-Macromolecule #4: TETRADECANE
Macromolecule | Name: TETRADECANE / type: ligand / ID: 4 / Number of copies: 6 / Formula: C14 |
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Molecular weight | Theoretical: 198.388 Da |
Chemical component information | ![]() ChemComp-C14: |
-Macromolecule #5: UNDECANE
Macromolecule | Name: UNDECANE / type: ligand / ID: 5 / Number of copies: 10 / Formula: UND |
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Molecular weight | Theoretical: 156.308 Da |
Chemical component information | ![]() ChemComp-UND: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 26 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 4326 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7b4l: |