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- PDB-8dmk: Cryo-EM reveals the molecular basis of laminin polymerization and... -

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Basic information

Entry
Database: PDB / ID: 8dmk
TitleCryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies
Components
  • Laminin subunit alpha-1
  • Laminin subunit beta-1
  • Laminin subunit gamma-1
KeywordsSTRUCTURAL PROTEIN / Laminin / Complex / Basement membrane
Function / homology
Function and homology information


laminin-3 complex / laminin complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin-11 complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / L1CAM interactions ...laminin-3 complex / laminin complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin-11 complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / L1CAM interactions / retinal blood vessel morphogenesis / morphogenesis of an epithelial sheet / hemidesmosome assembly / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / Laminin interactions / EGR2 and SOX10-mediated initiation of Schwann cell myelination / protein complex involved in cell-matrix adhesion / branching involved in salivary gland morphogenesis / Formation of the dystrophin-glycoprotein complex (DGC) / endoderm development / establishment of epithelial cell apical/basal polarity / negative regulation of cell adhesion / odontogenesis / extracellular matrix structural constituent / MET activates PTK2 signaling / positive regulation of muscle cell differentiation / maintenance of blood-brain barrier / epithelial tube branching involved in lung morphogenesis / endodermal cell differentiation / basement membrane / Non-integrin membrane-ECM interactions / regulation of embryonic development / extracellular matrix disassembly / ECM proteoglycans / Degradation of the extracellular matrix / embryo implantation / extracellular matrix / positive regulation of cell adhesion / substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of epithelial cell proliferation / Post-translational protein phosphorylation / integrin binding / 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 / protein-containing complex assembly / cell surface receptor signaling pathway / protein phosphorylation / cell adhesion / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / extracellular space / extracellular exosome / extracellular region / nucleus / membrane
Similarity search - Function
: / LAMB1-4 helical domain / Laminin IV type B / Laminin IV type B domain / Laminin IV type A domain profile. / Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV ...: / LAMB1-4 helical domain / Laminin IV type B / Laminin IV type B domain / Laminin IV type A domain profile. / Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / : / Laminin/attractin EGF domain / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Galactose-binding domain-like / Epidermal growth factor-like domain. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Laminin subunit beta-1 / Laminin subunit gamma-1 / Laminin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKulczyk, A.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: 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
DepositionJul 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Laminin subunit alpha-1
B: Laminin subunit beta-1
G: Laminin subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0589
Polymers103,9123
Non-polymers1,1466
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Laminin subunit alpha-1 / Laminin A chain / Laminin-1 subunit alpha / Laminin-3 subunit alpha / S-laminin subunit alpha / S-LAM alpha


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
#2: Protein Laminin subunit beta-1 / Laminin B1 chain / Laminin-1 subunit beta / Laminin-10 subunit beta / Laminin-12 subunit beta / ...Laminin B1 chain / Laminin-1 subunit beta / Laminin-10 subunit beta / Laminin-12 subunit beta / Laminin-2 subunit beta / Laminin-6 subunit beta / Laminin-8 subunit beta


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 Laminin subunit gamma-1


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 / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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
Molecular weightValue: 0.172 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 1.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategory
1cryoSPARC3particle selection
2SerialEMimage acquisition
4cryoSPARC3CTF correction
9cryoSPARC3initial Euler assignment
10cryoSPARC3final Euler assignment
11cryoSPARC3classification
12cryoSPARC33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125011 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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