7JZJ: Matrix protein VP40

Crystal structure demonstrating CTD-CTD interactions of Zaire Ebola virus VP40 dimer. Determined by X-ray diffraction at 2.46 Å resolution. Released 28 Oct 2020.

Method: X-ray diffraction
Resolution: 2.46 Å
Organism: Zaire ebolavirus (strain Mayinga-76)
Chains: 4
Atoms: 7,447
Mol. weight: 129.63 kDa
Released: 28 Oct 2020

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

Secondary structure: helices and β-sheets

7JZJ contains 43 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: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	46-50	5
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	148-152	5
β-strand	154-158	5	1
α-helix	159-162	4
β-strand	173-185	13	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
α-helix	244-246	3
β-strand	248-249	2	3
β-strand	253	1	3
α-helix	254-256	3
β-strand	258-262	5	3
α-helix	263-264	2
α-helix	265-272	8
β-strand	284-288	5	3
β-strand	304-309	6	4

Chain B: 14 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	70-83	14	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	148-152	5
β-strand	154-158	5	5
α-helix	159-162	4
β-strand	173-186	14	6
α-helix	187	1
β-strand	190	1	7
β-strand	204-208	5	8
α-helix	214-215	2
β-strand	216-217	2	8
α-helix	218-219	2
α-helix	234-243	10
α-helix	244-246	3
β-strand	248-253	6	7
α-helix	254-256	3
β-strand	258-262	5	7
α-helix	263-264	2
α-helix	265-272	8
β-strand	284-288	5	7
α-helix	296-298	3
β-strand	304-308	5	8

Chain C: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	51	1	9
β-strand	54-55	2	6
α-helix	61-64	4
β-strand	71-81	11	6
β-strand	92-101	10	6
α-helix	108-116	9
β-strand	119-125	7	9
β-strand	132-138	7	9
α-helix	148-152	5
β-strand	154-157	4	9
α-helix	159-162	4
β-strand	174-185	12	6
β-strand	190	1	10
β-strand	203-208	6	11
α-helix	214-215	2
β-strand	216-217	2	11
α-helix	218-219	2
α-helix	234-243	10
β-strand	248-253	6	10
β-strand	258-262	5	10
α-helix	265-270	6
β-strand	284-288	5	10
β-strand	304-309	6	11
β-strand	319	1	9

Chain D: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	46-50	5
β-strand	51	1	12
β-strand	54-55	2	13
α-helix	61-64	4
β-strand	71-83	13	13
β-strand	86-87	2	13
β-strand	92-101	10	13
α-helix	108-116	9
β-strand	119-124	6	12
β-strand	132-138	7	12
α-helix	148-152	5
β-strand	154-158	5	12
α-helix	159-162	4
β-strand	173-185	13	13
β-strand	203-208	6	14
β-strand	216-217	2	14
α-helix	218-219	2
α-helix	238-244	7
β-strand	248-253	6	15
α-helix	254-256	3
β-strand	258-262	5	15
α-helix	265-270	6
β-strand	284-288	5	15
β-strand	304-309	6	14
β-strand	319-320	2	12
α-helix	321-322	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Matrix protein VP40	A, B, C, D	protein	297	Zaire ebolavirus (strain Mayinga-76)	Q05128 (AlphaFold model)

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

>7JZJ_1 Matrix protein VP40 (chains A, B, C, D)
MAHHHHHHVDDDDNGDTPSNPLRPIADDTIDHASHTPGSVSSAFILEAMVNVISGPKVLM
KQIPIWLPLGVADQKTYSFDSTTAAIMLASYTITHFGKATNPLVRVNRLGPGIPDHPLRL
LRIGNQAFLQEFVLPPVQLPQYFTFDLTALKLITQPLPAATWTDDTPTGSNGALRPGISF
HPKLRPILLPNKSGKKGNSADLTSPEKIQAIMTSLQDFKIVPIDPTKNIMGIEVPETLVH
KLTGKKVTSKNGQPIIPVLLPKYIGLDPVAPGDLTMVITQDCDTCHSPASLPAVIEK

Primary citation

Ebola and Marburg virus matrix layers are locally ordered assemblies of VP40 dimers. Wan, W., Clarke, M., Norris, M.J. et al. Elife (2020) 9. DOI 10.7554/eLife.59225 · 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
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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