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Open data
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Basic information
Entry | Database: PDB / ID: 8em4 | ||||||
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Title | Cryo-EM structure of LRP2 at pH 7.5 | ||||||
![]() | Low-density lipoprotein receptor-related protein 2 | ||||||
![]() | MEMBRANE PROTEIN / LRP2 / Megalin / GP330 / Endocytosis | ||||||
Function / homology | ![]() Transport of RCbl within the body / endocytic hemoglobin import into cell / diol metabolic process / chemoattraction of axon / positive regulation of lipoprotein transport / pulmonary artery morphogenesis / secondary heart field specification / Retinoid metabolism and transport / positive regulation of oligodendrocyte progenitor proliferation / folate import across plasma membrane ...Transport of RCbl within the body / endocytic hemoglobin import into cell / diol metabolic process / chemoattraction of axon / positive regulation of lipoprotein transport / pulmonary artery morphogenesis / secondary heart field specification / Retinoid metabolism and transport / positive regulation of oligodendrocyte progenitor proliferation / folate import across plasma membrane / metal ion transport / response to leptin / ventricular compact myocardium morphogenesis / protein transporter activity / Cargo recognition for clathrin-mediated endocytosis / hormone binding / vitamin D metabolic process / neuron projection arborization / Clathrin-mediated endocytosis / hormone secretion / coronary artery morphogenesis / outflow tract septum morphogenesis / coronary vasculature development / insulin-like growth factor I binding / transcytosis / protein import / aorta development / cargo receptor activity / ventricular septum development / positive regulation of neurogenesis / endosomal transport / low-density lipoprotein particle receptor binding / hemoglobin binding / amyloid-beta clearance / positive regulation of endocytosis / brush border / vagina development / negative regulation of BMP signaling pathway / response to X-ray / endocytic vesicle / axonal growth cone / clathrin-coated pit / forebrain development / receptor-mediated endocytosis / kidney development / neural tube closure / PDZ domain binding / endosome lumen / nuclear receptor binding / brush border membrane / sensory perception of sound / cellular response to growth factor stimulus / SH3 domain binding / endocytosis / male gonad development / protein transport / apical part of cell / heart development / protein-folding chaperone binding / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome / membrane raft / apical plasma membrane / external side of plasma membrane / axon / calcium ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å | ||||||
![]() | Beenken, A. / Cerutti, G. / Brasch, J. / Fitzpatrick, A.W. / Barasch, J. / Shapiro, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of LRP2 reveal a molecular machine for endocytosis. Authors: Andrew Beenken / Gabriele Cerutti / Julia Brasch / Yicheng Guo / Zizhang Sheng / Hediye Erdjument-Bromage / Zainab Aziz / Shelief Y Robbins-Juarez / Estefania Y Chavez / Goran Ahlsen / ...Authors: Andrew Beenken / Gabriele Cerutti / Julia Brasch / Yicheng Guo / Zizhang Sheng / Hediye Erdjument-Bromage / Zainab Aziz / Shelief Y Robbins-Juarez / Estefania Y Chavez / Goran Ahlsen / Phinikoula S Katsamba / Thomas A Neubert / Anthony W P Fitzpatrick / Jonathan Barasch / Lawrence Shapiro / ![]() Abstract: The low-density lipoprotein (LDL) receptor-related protein 2 (LRP2 or megalin) is representative of the phylogenetically conserved subfamily of giant LDL receptor-related proteins, which function in ...The low-density lipoprotein (LDL) receptor-related protein 2 (LRP2 or megalin) is representative of the phylogenetically conserved subfamily of giant LDL receptor-related proteins, which function in endocytosis and are implicated in diseases of the kidney and brain. Here, we report high-resolution cryoelectron microscopy structures of LRP2 isolated from mouse kidney, at extracellular and endosomal pH. The structures reveal LRP2 to be a molecular machine that adopts a conformation for ligand binding at the cell surface and for ligand shedding in the endosome. LRP2 forms a homodimer, the conformational transformation of which is governed by pH-sensitive sites at both homodimer and intra-protomer interfaces. A subset of LRP2 deleterious missense variants in humans appears to impair homodimer assembly. These observations lay the foundation for further understanding the function and mechanism of LDL receptors and implicate homodimerization as a conserved feature of the LRP receptor subfamily. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 183.3 KB | Display | |
Data in CIF | ![]() | 298.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28233MC ![]() 8em7C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 519746.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Polysaccharide | #3: Sugar | ChemComp-NGA / #4: Sugar | ChemComp-NAG / #5: Chemical | ChemComp-CA / 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 |
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Sample preparation
Component | Name: LRP2 at neutral pH / Type: COMPLEX / Details: Endogenously purified from mouse kidney / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 54.87 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||
3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 492737 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT |