6JLB | pdb_00006jlb

Crystal structure of lamin A/C fragment and assembly mechanisms of intermediate filaments

• PDB DOI: https://doi.org/10.2210/pdb6JLB/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-03-04 Released: 2019-09-11 
• Deposition Author(s): Ahn, J., Jo, I., Ha, N.C.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 
  0.261 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Structural basis for lamin assembly at the molecular level.

Ahn, J., Jo, I., Kang, S.M., Hong, S., Kim, S., Jeong, S., Kim, Y.H., Park, B.J., Ha, N.C.

(2019) Nat Commun 10: 3757-3757

• PubMed: 31434876 
• DOI: https://doi.org/10.1038/s41467-019-11684-x
• Primary Citation Related Structures: 
  6JLB


• PubMed Abstract: 
  

  Nuclear structure and function are governed by lamins, which are intermediate filaments that mostly consist of α-helices. Different lamin assembly models have been proposed based on low resolution and fragmented structures. However, their assembly mechanisms are still poorly understood at the molecular level. Here, we present the crystal structure of a long human lamin fragment at 3.2 Å resolution that allows the visualization of the features of the full-length protein. The structure shows an anti-parallel arrangement of the two coiled-coil dimers, which is important for the assembly process. We further discover an interaction between the lamin dimers by using chemical cross-linking and mass spectrometry analysis. Based on these two interactions, we propose a molecular mechanism for lamin assembly that is in agreement with a recent model representing the native state and could explain pathological mutations. Our findings also provide the molecular basis for assembly mechanisms of other intermediate filaments.

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Organizational Affiliation: 
• Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Korea.
Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Korea.
Department of Microbiology, Catholic University of Daegu School of Medicine, Daegu, 38430, Korea.
Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Korea. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 140.22 kDa 
• Atom Count: 7,161 
• Modeled Residue Count: 886 
• Deposited Residue Count: 1,216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lamin A/C	A, B, C, D	304	Homo sapiens	Mutation(s): 0  Gene Names: LMNA, LMN1
UniProt & NIH Common Fund Data Resources
Find proteins for P02545 (Homo sapiens) Explore P02545  Go to UniProtKB:  P02545
PHAROS:  P02545 GTEx:  ENSG00000160789

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free:  0.261 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 231.267	α = 90
b = 84.997	β = 90
c = 92.383	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
SHELXCD	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Ahn, J., Jo, I., Ha, N.C.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017R1A2B2003992
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017M3A9F6029736

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary