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Yorodumi- PDB-7x2u: Structure of a human NHE3-CHP1 complex in the autoinhibited state -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x2u | ||||||
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Title | Structure of a human NHE3-CHP1 complex in the autoinhibited state | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Sodium/proton antiporter | ||||||
Function / homology | Function and homology information positive regulation of sodium:proton antiporter activity / Sodium/Proton exchangers / negative regulation of phosphatase activity / transporter complex / positive regulation of protein glycosylation / Hyaluronan uptake and degradation / membrane docking / positive regulation of phospholipid biosynthetic process / negative regulation of protein autophosphorylation / potassium:proton antiporter activity ...positive regulation of sodium:proton antiporter activity / Sodium/Proton exchangers / negative regulation of phosphatase activity / transporter complex / positive regulation of protein glycosylation / Hyaluronan uptake and degradation / membrane docking / positive regulation of phospholipid biosynthetic process / negative regulation of protein autophosphorylation / potassium:proton antiporter activity / sodium:proton antiporter activity / positive regulation of protein transport / cellular response to acidic pH / membrane organization / sodium ion import across plasma membrane / microtubule bundle formation / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of protein import into nucleus / small GTPase-mediated signal transduction / negative regulation of NF-kappaB transcription factor activity / protein kinase inhibitor activity / brush border / endoplasmic reticulum-Golgi intermediate compartment / potassium channel regulator activity / positive regulation of protein targeting to membrane / monoatomic ion transport / cytoplasmic microtubule organization / transport vesicle / potassium ion transmembrane transport / negative regulation of protein ubiquitination / protein export from nucleus / negative regulation of protein phosphorylation / PDZ domain binding / regulation of intracellular pH / brush border membrane / negative regulation of protein kinase activity / potassium ion transport / kinase binding / calcium-dependent protein binding / microtubule cytoskeleton / microtubule binding / membrane => GO:0016020 / membrane fusion / protein stabilization / membrane raft / apical plasma membrane / Golgi membrane / focal adhesion / calcium ion binding / cell surface / endoplasmic reticulum / extracellular exosome / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Dong, Y. / Li, H. / Gao, Y. / Zhang, X.C. / Zhao, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structure of a human NHE3-CHP1 complex in the autoinhibited state Authors: Dong, Y. / Li, H. / Ilie, A. / Gao, Y. / Boucher, A. / Zhang, X.C. / Orlowski, J. / Zhao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x2u.cif.gz | 274.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x2u.ent.gz | 215.8 KB | Display | PDB format |
PDBx/mmJSON format | 7x2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x2u_validation.pdf.gz | 1023.4 KB | Display | wwPDB validaton report |
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Full document | 7x2u_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7x2u_validation.xml.gz | 46 KB | Display | |
Data in CIF | 7x2u_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/7x2u ftp://data.pdbj.org/pub/pdb/validation_reports/x2/7x2u | HTTPS FTP |
-Related structure data
Related structure data | 32971MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 70537.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A3, NHE3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P48764 #2: Protein | Mass: 21411.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHP1, CHP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q99653 #3: Chemical | #4: Chemical | ChemComp-PGT / ( Has ligand of interest | Y | |
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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 NHE3-CHP1 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 |
Buffer solution | pH: 7.5 |
Specimen | 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 / Nominal defocus max: 22000 nm / Nominal defocus min: 12000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37572 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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