6YJD: Capsid assembly scaffolding protein,Prelamin-A/C

Lamin A coil2 dimer stabilized by N-terminal capping. Determined by X-ray diffraction at 2.9 Å resolution. Released 24 Feb 2021.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Bacillus phage phi29, Homo sapiens
Chains: 1
Atoms: 844
Mol. weight: 15.29 kDa
Ligands: NI
Released: 24 Feb 2021

Explore 6YJD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YJD contains 3 α-helices and 0 β-strands across 1 chain. 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	279-281	3
α-helix	282-293	12
α-helix	299-379	81

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid assembly scaffolding protein,Prelamin-A/C	A	protein	127	Bacillus phage phi29, Homo sapiens	P02545 (AlphaFold model), P13848

Sequence of entity 1 (A), FASTA

>6YJD_1 Capsid assembly scaffolding protein,Prelamin-A/C (chains A)
GMPLKPEEHEDILNKLLDPELAQSERTEALQQLRVNYGSCVSEYNDLTKSLARERDTSRR
LLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEGEEERLRLSPSPTSQ
RSRGRAS

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	2

Water and common crystallization additives (CL, TRS) are not listed.

Primary citation

Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions. Stalmans, G., Lilina, A.V., Vermeire, P.J. et al. Cells (2020) 9. DOI 10.3390/cells9071633 · PubMed

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…
7YVD 2.1 Å, The crystal structure of the progerin C-terminal peptide and the Ig-like domain of lamin…
1X8Y 2.2 Å, Human lamin coil 2B

Browse structure collections

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