7JZT: Matrix protein VP40

Low resolution crystal structure of Zaire Ebola virus VP40 in space group P6422. Determined by X-ray diffraction at 3.77 Å resolution. Released 21 Oct 2020.

Method: X-ray diffraction
Resolution: 3.77 Å
Organism: Zaire ebolavirus (strain Mayinga-76)
Chains: 4
Atoms: 6,795
Mol. weight: 128.98 kDa
Released: 21 Oct 2020

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

Secondary structure: helices and β-sheets

7JZT contains 40 α-helices and 65 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: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	1
β-strand	54-55	2	2
α-helix	61-64	4
β-strand	71	1	3
β-strand	72-83	12	2
β-strand	86-100	15	2
α-helix	108-116	9
β-strand	122-124	3	1
β-strand	132-135	4	1
α-helix	148-152	5
β-strand	155-158	4	1
β-strand	173-174	2	2
β-strand	180-182	3	2
β-strand	185	1	3
β-strand	206-207	2	4
α-helix	214-215	2
β-strand	216-217	2	4
α-helix	234-236	3
α-helix	237-243	7
β-strand	258-260	3	5
α-helix	262-264	3
α-helix	267	1
α-helix	268-272	5
β-strand	286-288	3	5
β-strand	306	1	4

Chain B: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	48-50	3
β-strand	51	1	6
β-strand	54-55	2	7
α-helix	61-64	4
β-strand	71-83	13	7
β-strand	86-95	10	7
β-strand	99-101	3	7
α-helix	108-116	9
β-strand	120-123	4	6
β-strand	132	1	8
β-strand	134-137	4	6
α-helix	148-152	5
β-strand	158	1	8
α-helix	159-162	4
α-helix	164	1
β-strand	175-185	11	7
α-helix	186-187	2
β-strand	206-208	3	9
β-strand	217	1	9
α-helix	234-236	3
α-helix	237-246	10
β-strand	249-251	3	10
α-helix	254-256	3
β-strand	258-262	5	10
α-helix	265-271	7
β-strand	284-288	5	10
β-strand	304-306	3	9

Chain C: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	51	1	11
β-strand	54-55	2	12
α-helix	61-64	4
β-strand	72-82	11	12
β-strand	83	1	13
β-strand	86	1	13
β-strand	92-100	9	12
α-helix	108-117	10
β-strand	120-125	6	11
β-strand	132-137	6	11
α-helix	141-142	2
α-helix	148-152	5
β-strand	154-158	5	11
α-helix	159-162	4
β-strand	173-182	10	12
α-helix	185-187	3
β-strand	206-207	2	14
β-strand	216-217	2	14
α-helix	234-241	8
α-helix	244-246	3
β-strand	249-251	3	15
α-helix	254-256	3
β-strand	258-261	4	15
α-helix	265-271	7
α-helix	282-283	2
β-strand	285-288	4	15
β-strand	305-306	2	14

Chain D: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	16
α-helix	48-50	3
β-strand	51	1	17
β-strand	54-55	2	18
α-helix	61-64	4
β-strand	71-83	13	18
β-strand	86-100	15	18
α-helix	108-117	10
β-strand	120	1	17
β-strand	121-125	5	16
β-strand	132-136	5	16
α-helix	148-152	5
β-strand	157-158	2	16
α-helix	159-162	4
β-strand	175-185	11	18
β-strand	190	1	19
β-strand	207	1	20
α-helix	214-215	2
β-strand	216	1	20
α-helix	237-240	4
α-helix	241-243	3
β-strand	249-251	3	21
α-helix	254-256	3
β-strand	258-261	4	21
β-strand	284	1	19
β-strand	286-288	3	21

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

>7JZT_1 Matrix protein VP40 (chains A, B, C, D)
MAHHHHHHVDDDDKGDTPSNPLRPIADDTIDHASHTPGSVSSAFILEAMVNVISGPKVLM
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
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
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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