7YVD | pdb_00007yvd

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)

Experimental Data Snapshot

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

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02545
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SEC (Subject of Investigation/LOI) Query on SEC Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	SELENOCYSTEINE C₃ H₇ N O₂ Se ZKZBPNGNEQAJSX-REOHCLBHSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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), 0.195 (DCC)
R-Value Work: 0.164 (Depositor), 0.164 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-30

Deposition Author(s):

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 (Full details and data files)

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
Version 1.3: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.