4LDD: Ebola virus VP40 Hexamer

Crystal Structure of Ebola virus VP40 Hexamer. Determined by X-ray diffraction at 3.5 Å resolution. Released 21 Aug 2013.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Ebola virus
Chains: 3
Atoms: 3,883
Mol. weight: 96.73 kDa
Released: 21 Aug 2013

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

Secondary structure: helices and β-sheets

4LDD contains 15 α-helices and 30 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	51	1	6
β-strand	54-55	2	7
α-helix	61-63	3
β-strand	70-82	13	7
β-strand	89-101	13	7
α-helix	108-116	9
β-strand	120-124	5	6
β-strand	132-137	6	6
α-helix	148-152	5
β-strand	154-158	5	6
α-helix	159-162	4
β-strand	173-186	14	7

Chain B: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	51	1	1
β-strand	54-55	2	2
α-helix	61-63	3
β-strand	70-83	14	2
β-strand	86-101	16	2
α-helix	108-116	9
β-strand	120-124	5	1
β-strand	132-137	6	1
α-helix	148-152	5
β-strand	154-158	5	1
α-helix	159-162	4
β-strand	173-186	14	2
β-strand	204-206	3	3
β-strand	217	1	3
α-helix	234-243	10
α-helix	244-246	3
β-strand	248-253	6	4
β-strand	258-262	5	4
α-helix	265-270	6
β-strand	284-286	3	4
β-strand	306-308	3	3

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	51	1	5
β-strand	54-55	2	2
α-helix	61-63	3
β-strand	70-83	14	2
β-strand	86-101	16	2
α-helix	108-116	9
β-strand	120-124	5	5
β-strand	132-137	6	5
α-helix	148-152	5
β-strand	154-158	5	5
α-helix	159-162	4
β-strand	173-186	14	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Matrix protein VP40	A, B, C	protein	297	Ebola virus	Q05128 (AlphaFold model)

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

>4LDD_1 Matrix protein VP40 (chains A, B, C)
MAHHHHHHVDDDDKGDTPSNPLRPIADDTIDHASHTPGSVSSAFILEAMVNVISGPKVLM
KQIPIWLPLGVADQKTYSFDSTTAAIMLASYTITHFGKATNPLVRVNRLGPGIPDHPLRL
LRIGNQAFLQEFVLPPVQLPQYFTFDLTALKLITQPLPAATWTDDTPTGSNGALRPGISF
HPKLRPILLPNKSGKKGNSADLTSPEKIQAIMTSLQDFKIVPIDPTKNIMGIEVPETLVH
KLTGKKVTSKNGQPIIPVLLPKYIGLDPVAPGDLTMVITQDCDTCHSPASLPAVIEK

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
4LDM 1.85 Å, Crystal Structure of an RNA-free VP40 Octameric Ring
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
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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