7YVD

The crystal structure of the progerin C-terminal peptide and the Ig-like domain of lamin A/C

• PDB DOI: https://doi.org/10.2210/pdb7YVD/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2022-08-19 Released: 2023-08-30 
• Deposition Author(s): Ahn, J., Ha, N.C.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

The crystal structure of the progerin C-terminal peptide and the Ig-like domain of lamin A/C

Ahn, J., Ha, N.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.75 kDa 
• Atom Count: 3,511 
• Modelled Residue Count: 392 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lamin-A/C	A, B, C	132	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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SEC (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	SELENOCYSTEINE C3 H7 N O2 Se ZKZBPNGNEQAJSX-REOHCLBHSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.974	α = 90
b = 91.974	β = 90
c = 204.562	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-30 
Deposition Author(s): Ahn, J., Ha, N.C.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020R1A4A101932213
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1I1A1A01049976

Revision History  

• Version 1.0: 2023-08-30
  Type: Initial release
  
• Version 1.1: 2023-11-15
  Changes: Data collection
• Version 1.2: 2024-10-23
  Changes: Structure summary