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Yorodumi- PDB-7b4m: CryoEM structure of the human sodium proton exchanger NHA2 in nanodisc -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b4m | ||||||
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Title | CryoEM structure of the human sodium proton exchanger NHA2 in nanodisc | ||||||
Components | Sodium/hydrogen exchanger 9B2 | ||||||
Keywords | MEMBRANE 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 / flagellated sperm motility / sodium ion homeostasis / 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 / flagellated sperm motility / sodium ion homeostasis / 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 / mitochondrial membrane / Stimuli-sensing channels / recycling endosome / synaptic vesicle membrane / recycling endosome membrane / monoatomic ion transmembrane transport / basolateral plasma membrane / mitochondrial inner membrane / apical plasma membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å | ||||||
Authors | Woehlert, D. / Kuhlbrandt, W. / Yildiz, O. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: CryoEM structure of the human sodium proton exchanger NHA2 in nanodisc Authors: Woehlert, D. / Kuhlbrandt, W. / Yildiz, O. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7b4m.cif.gz | 161.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b4m.ent.gz | 124.3 KB | Display | PDB format |
PDBx/mmJSON format | 7b4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b4m_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7b4m_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7b4m_validation.xml.gz | 44.4 KB | Display | |
Data in CIF | 7b4m_validation.cif.gz | 63.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/7b4m ftp://data.pdbj.org/pub/pdb/validation_reports/b4/7b4m | HTTPS FTP |
-Related structure data
Related structure data | 12003MC 7b4lC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human sodium proton exchanger NHA2 in nanodisc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.15 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1251 |
Image scans | Movie frames/image: 40 |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 285970 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47284 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Refine LS restraints |
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