8DMK

Cryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies

PDB DOI: https://doi.org/10.2210/pdb8DMK/pdb
EM Map EMD-27542: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-07-08 Released: 2023-02-01
Deposition Author(s): Kulczyk, A.W.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM reveals the molecular basis oflaminin polymerization and LN-lamininopathies.

Kulczyk, A.W., McKee, K.K., Zhang, X., Bizukojc, I., Yu, Y.Q., Yurchenco, P.D.

(2023) Nat Commun 14: 317-317

PubMed: 36658135 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-36077-z
Primary Citation of Related Structures:
8DMK

PubMed 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 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.

Organizational Affiliation

Institute for Quantitative Biomedicine, Department of Biochemistry and Microbiology, Rutgers University, Piscataway, NJ, 08854, USA. arek.kulczyk@rutgers.edu.

Macromolecule Content

Total Structure Weight: 105.06 kDa
Atom Count: 7,348
Modelled Residue Count: 917
Deposited Residue Count: 917
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laminin subunit alpha-1	A	305	Homo sapiens	Mutation(s): 0 Gene Names: Lama1, Lama, Lama-1
UniProt & NIH Common Fund Data Resources
Find proteins for P19137 (Mus musculus) Explore P19137 Go to UniProtKB: P19137
IMPC: MGI:99892
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19137
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Laminin subunit beta-1	B	307	Homo sapiens	Mutation(s): 0 Gene Names: LAMB1
UniProt & NIH Common Fund Data Resources
Find proteins for P07942 (Homo sapiens) Explore P07942 Go to UniProtKB: P07942
PHAROS: P07942 GTEx: ENSG00000091136
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07942
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Laminin subunit gamma-1	C [auth G]	305	Homo sapiens	Mutation(s): 0 Gene Names: LAMC1
UniProt & NIH Common Fund Data Resources
Find proteins for P11047 (Homo sapiens) Explore P11047 Go to UniProtKB: P11047
PHAROS: P11047 GTEx: ENSG00000135862
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11047
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G SDF format, chain H [auth G] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G MOL2 format, chain H [auth G]	D [auth A], E [auth A], F [auth B], G, H [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G Focus chain H [auth G] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G Focus chain H [auth G]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth G] MOL2 format, chain I [auth G]	I [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth G] Interactions & Density Focus chain I [auth G]