4LDM: RNA-free VP40 Octameric Ring

Crystal Structure of an RNA-free VP40 Octameric Ring. Determined by X-ray diffraction at 1.85 Å resolution. Released 21 Aug 2013.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Ebola virus
Chains: 1
Atoms: 1,035
Mol. weight: 17.5 kDa
Released: 21 Aug 2013

Explore 4LDM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LDM contains 3 α-helices and 6 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, 6 β-strands

Element	Residues	Length	Sheet
β-strand	71-84	14	1
β-strand	87-101	15	1
α-helix	108-117	10
β-strand	120-125	6	1
β-strand	132-137	6	1
α-helix	148-151	4
β-strand	154-158	5	1
α-helix	159-162	4
β-strand	173-185	13	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Matrix protein VP40	A	protein	159	Ebola virus	Q05128 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4LDM_1 Matrix protein VP40 (chains A)
MAHHHHHHVDDDDKGDTPSNPLRPIADDTIDHASHTPGSVSSAFILEAMVNVISGPKVLM
KQIPIWLPLGVADQKTYSFDSTTAAIMLASYTITHFGKATNPLVRVNRLGPGIPDHPLRL
LRIGNQAFLQEFVLPPVQLPQYFTFDLTALKLITQPLPA

Primary citation

Structural Rearrangement of Ebola Virus VP40 Begets Multiple Functions in the Virus Life Cycle. Bornholdt, Z.A., Noda, T., Abelson, D.M. et al. Cell (2013) 154:763-774. DOI 10.1016/j.cell.2013.07.015 · PubMed

Other PDB entries of the same protein (UniProt Q05128 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7K5L 1.38 Å, Ebola virus VP40 octameric ring generated by an RNA oligonucleotide
1H2C 1.6 Å, Ebola virus matrix protein VP40 N-terminal domain in complex with RNA (High-resolution…
7K5D 1.78 Å, Ebola virus VP40 octameric ring generated by a DNA oligonucleotide
4EJE 2.2 Å, Structure Of The Tsg101 UEV Domain In Complex With an Ebola PTAP late Domain Peptide
7JZJ 2.46 Å, Crystal structure demonstrating CTD-CTD interactions of Zaire Ebola virus VP40 dimer
1H2D 2.6 Å, Ebola virus matrix protein VP40 N-terminal domain in complex with RNA (Low-resolution…
4LDB 3.1 Å, Crystal Structure of Ebola Virus VP40 Dimer
4LDD 3.5 Å, Crystal Structure of Ebola virus VP40 Hexamer
7JZT 3.77 Å, Low resolution crystal structure of Zaire Ebola virus VP40 in space group P6422
4LDI 4.15 Å, Low resolution structure of Ebola virus M241R mutant
2KQ0 Human NEDD4 3rd WW Domain Complex with Ebola Zaire Virus Matrix Protein VP40 Derived…

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