7YVD: Lamin-A/C

The crystal structure of the progerin C-terminal peptide and the Ig-like domain of lamin A/C. Determined by X-ray diffraction at 2.1 Å resolution. Released 30 Aug 2023.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,511
Mol. weight: 44.75 kDa
Ligands: SEC
Released: 30 Aug 2023

Explore 7YVD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YVD contains 8 α-helices and 36 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	424-436	13	1
β-strand	440-445	6	2
β-strand	451-456	6	2
β-strand	462-463	2	3
β-strand	468-473	6	1
α-helix	477-478	2
β-strand	479-482	4	1
β-strand	488-489	2	3
β-strand	494-499	6	2
α-helix	500-502	3
β-strand	507	1	2
β-strand	511-514	4	2
β-strand	525-531	7	1
β-strand	537-549	13	1

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	426-436	11	1
β-strand	440-445	6	4
β-strand	451-456	6	4
β-strand	462-463	2	5
β-strand	468-472	5	1
α-helix	477-478	2
β-strand	479-482	4	1
β-strand	488-489	2	5
β-strand	494-499	6	4
α-helix	500-502	3
α-helix	504-506	3
β-strand	507	1	4
β-strand	511-514	4	4
β-strand	525-531	7	1
β-strand	537-549	13	1

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	424-436	13	1
β-strand	440-445	6	6
β-strand	451-456	6	6
β-strand	462-463	2	7
β-strand	468-473	6	1
α-helix	477-478	2
β-strand	479-482	4	1
β-strand	488-489	2	7
β-strand	494-499	6	6
α-helix	500-502	3
β-strand	507	1	6
β-strand	511-514	4	6
β-strand	525-531	7	1
β-strand	537-549	13	1
α-helix	550-551	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lamin-A/C	A, B, C	protein	132	Homo sapiens	P02545 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>7YVD_1 Lamin-A/C (chains A, B, C)
LESTESRSSFSQHARTSGRVAVEEVDEEGKFVRLRNKSNEDQSMGNWQIKRQNGDDPLLT
YRFPPKFTLKAGQVVTIWAAGAGATHSPPTDLVWKAQNTWGCGNSLRTALINSTGEEVAM
RKLVRSVTVVED

Ligands and cofactors

ID	Name	Formula	Copies
SEC	Selenocysteine	C3 H7 N O2 Se	3

Primary citation

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.

Other PDB entries of the same protein (UniProt P02545 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7WZZ 1.3 Å, Crystal structure of peptide KAGQVVTIW in complex with HLA-B5801
7X1B 1.4 Å, Crystal structure of peptide KAGQVVTI in complex with HLA-B5801
1IFR 1.4 Å, Structure of Lamin A/C Globular Domain
3GEF 1.5 Å, Crystal structure of the R482W mutant of lamin A/C
8I33 1.62 Å, Coil 1a of lamin A (residue 25-65)
7Z21 1.63 Å, BAF A12T bound to the lamin A/C Ig-fold domain
7CRG 1.8 Å, Beta-strand-mediated dimeric formation of the extended Ig-like domains of human lamin A/C
7X5D 1.82 Å, Crystal Structure of the K316C mutant of Human Lamin A/C Coil 2 (residues 244-340)
6YF5 1.83 Å, Lamin A 17-70 coil1A dimer stabilized by C-terminal capping
6GHD 2.1 Å, Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies…
1X8Y 2.2 Å, Human lamin coil 2B
6RPR 2.26 Å, LEM domain of Emerin mutant T43I in complex with BAF dimer and the Igfold of the lamin A/C

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