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Yorodumi- PDB-8dmk: Cryo-EM reveals the molecular basis of laminin polymerization and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dmk | ||||||
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Title | Cryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Laminin / Complex / Basement membrane | ||||||
Function / homology | Function and homology information laminin-3 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin complex / laminin-1 complex / laminin-10 complex / retinal blood vessel morphogenesis / L1CAM interactions ...laminin-3 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin complex / laminin-1 complex / laminin-10 complex / retinal blood vessel morphogenesis / L1CAM interactions / regulation of basement membrane organization / morphogenesis of an epithelial sheet / hemidesmosome assembly / positive regulation of integrin-mediated signaling pathway / glycosphingolipid binding / tissue development / Laminin interactions / endoderm development / EGR2 and SOX10-mediated initiation of Schwann cell myelination / branching involved in salivary gland morphogenesis / protein complex involved in cell-matrix adhesion / establishment of epithelial cell apical/basal polarity / camera-type eye development / odontogenesis / blood vessel morphogenesis / extracellular matrix structural constituent / MET activates PTK2 signaling / maintenance of blood-brain barrier / epithelial tube branching involved in lung morphogenesis / endodermal cell differentiation / positive regulation of muscle cell differentiation / regulation of embryonic development / Non-integrin membrane-ECM interactions / basement membrane / positive regulation of cell adhesion / ECM proteoglycans / extracellular matrix disassembly / regulation of cell migration / extracellular matrix / Degradation of the extracellular matrix / substrate adhesion-dependent cell spreading / positive regulation of epithelial cell proliferation / axon guidance / Post-translational protein phosphorylation / animal organ morphogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cell-cell junction / cell migration / retina development in camera-type eye / collagen-containing extracellular matrix / protein-containing complex assembly / cell surface receptor signaling pathway / cell adhesion / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / protein phosphorylation / structural molecule activity / perinuclear region of cytoplasm / extracellular space / extracellular exosome / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Kulczyk, A.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM reveals the molecular basis oflaminin polymerization and LN-lamininopathies. Authors: Arkadiusz W Kulczyk / Karen K McKee / Ximo Zhang / Iwona Bizukojc / Ying Q Yu / Peter D Yurchenco / Abstract: Laminin polymerization is the major step in basement membranes assembly. Its failures cause laminin N-terminal domain lamininopathies including Pierson syndrome. We have employed cryo-electron ...Laminin polymerization is the major step in basement membranes assembly. Its failures cause laminin N-terminal domain lamininopathies including Pierson syndrome. We have employed cryo-electron microscopy to determine a 3.7 Å structure of the trimeric laminin polymer node containing α1, β1 and γ1 subunits. The structure reveals the molecular basis of calcium-dependent formation of laminin lattice, and provides insights into polymerization defects manifesting in human disease. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dmk.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dmk.ent.gz | 136.1 KB | Display | PDB format |
PDBx/mmJSON format | 8dmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/8dmk ftp://data.pdbj.org/pub/pdb/validation_reports/dm/8dmk | HTTPS FTP |
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-Related structure data
Related structure data | 27542MC 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: 34709.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lama1, Lama, Lama-1 / Production host: Homo sapiens (human) / References: UniProt: P19137 | ||||
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#2: Protein | Mass: 35091.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMB1 / Production host: Homo sapiens (human) / References: UniProt: P07942 | ||||
#3: Protein | Mass: 34110.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMC1 / Production host: Homo sapiens (human) / References: UniProt: P11047 | ||||
#4: Sugar | ChemComp-NAG / #5: Chemical | ChemComp-CA / | Has ligand of interest | N | |
-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: Lamimin polymer node / Type: COMPLEX Details: A trimeric complex of the N-terminal fragments (LN, LE1, LE2 domains) from laminin alpha 1, laminin beta 1 and laminin gamma 1. Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 0.172 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 1.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125011 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL |