4LDB: Ebola Virus VP40 Dimer

Crystal Structure of Ebola Virus VP40 Dimer. Determined by X-ray diffraction at 3.1 Å resolution. Released 21 Aug 2013.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Ebola virus
Chains: 4
Atoms: 7,574
Mol. weight: 128.98 kDa
Released: 21 Aug 2013

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

Secondary structure: helices and β-sheets

4LDB contains 46 α-helices and 63 β-strands across 4 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: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	47-50	4
β-strand	51	1	1
β-strand	54-55	2	2
α-helix	61-64	4
β-strand	71-83	13	2
β-strand	86-101	16	2
α-helix	108-116	9
β-strand	119-125	7	1
β-strand	132-138	7	1
α-helix	148-151	4
β-strand	154-158	5	1
α-helix	159-162	4
β-strand	173-185	13	2
α-helix	186-187	2
β-strand	190	1	3
β-strand	203-208	6	4
α-helix	214-215	2
β-strand	216-217	2	4
α-helix	234-243	10
β-strand	248-253	6	3
α-helix	254-256	3
β-strand	258-262	5	3
α-helix	263-264	2
α-helix	265-272	8
α-helix	274-276	3
β-strand	284-288	5	3
β-strand	304-309	6	4

Chain B: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	47-50	4
β-strand	51	1	5
β-strand	54-55	2	6
α-helix	61-64	4
β-strand	71-83	13	6
β-strand	86-101	16	6
α-helix	108-116	9
β-strand	119-125	7	5
β-strand	132-138	7	5
α-helix	148-151	4
β-strand	154-158	5	5
α-helix	159-162	4
β-strand	173-185	13	6
α-helix	186-187	2
β-strand	190	1	7
β-strand	203-208	6	8
α-helix	214-215	2
β-strand	216-217	2	8
α-helix	218	1
α-helix	234-243	10
β-strand	248-253	6	7
β-strand	258-262	5	7
α-helix	263-264	2
α-helix	265-272	8
β-strand	284-288	5	7
β-strand	304-309	6	8

Chain C: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	47-50	4
β-strand	51	1	9
β-strand	54-55	2	10
α-helix	61-64	4
β-strand	71-83	13	10
β-strand	86-87	2	10
β-strand	92-101	10	10
α-helix	108-116	9
β-strand	119-125	7	9
β-strand	132-138	7	9
α-helix	148-151	4
β-strand	154-158	5	9
α-helix	159-162	4
β-strand	173-185	13	10
α-helix	186-187	2
β-strand	190	1	11
β-strand	205-208	4	12
β-strand	216-217	2	12
α-helix	218-219	2
α-helix	235-242	8
α-helix	244-246	3
β-strand	248-253	6	11
α-helix	254-256	3
β-strand	258-262	5	11
α-helix	265-271	7
β-strand	284-288	5	11
β-strand	304-307	4	12
β-strand	319-320	2	9

Chain D: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	47-50	4
β-strand	51	1	13
β-strand	54-55	2	14
α-helix	61-64	4
β-strand	71-81	11	14
β-strand	92-101	10	14
α-helix	108-116	9
β-strand	119-125	7	13
β-strand	132-138	7	13
α-helix	148-151	4
β-strand	154-158	5	13
α-helix	159-162	4
β-strand	174-185	12	14
α-helix	186-187	2
β-strand	190	1	15
β-strand	204-208	5	16
β-strand	216-217	2	16
α-helix	218-219	2
α-helix	234-242	9
α-helix	244-246	3
β-strand	248-253	6	15
α-helix	254-256	3
β-strand	258-262	5	15
α-helix	265-268	4
α-helix	281-283	3
β-strand	284-288	5	15
β-strand	304-308	5	16
β-strand	319-320	2	13

Molecules and chains

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

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

>4LDB_1 Matrix protein VP40 (chains A, B, C, D)
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…
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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