8Y9J: Ebola virus nucleocapsid subunit

Structure of the Ebola virus nucleocapsid subunit. Determined by electron microscopy at 4.6 Å resolution. Released 29 Jan 2025.

Method: Electron microscopy
Resolution: 4.6 Å
Organisms: Zaire ebolavirus, Homo sapiens
Chains: 5
Atoms: 9,770
Mol. weight: 226.91 kDa
Released: 29 Jan 2025

Explore 8Y9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y9J contains 64 α-helices and 25 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: 20 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	24-28	5
β-strand	39-44	6	1
α-helix	49-63	15
α-helix	69-83	15
α-helix	86-90	5
α-helix	94-101	8
β-strand	104-109	6	1
α-helix	117-120	4
α-helix	125-136	12
α-helix	146-156	11
α-helix	164-182	19
α-helix	189-220	32
α-helix	227-239	13
α-helix	245-253	9
β-strand	255-257	3	2
β-strand	262-264	3	2
α-helix	266-269	4
α-helix	271-289	19
α-helix	294-300	7
α-helix	302-307	6
α-helix	314-328	15
α-helix	331-334	4
α-helix	338-365	28
α-helix	370-407	38

Chain B: 23 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	22-27	6
β-strand	39-45	7	3
α-helix	49-63	15
α-helix	67-82	16
α-helix	86-92	7
α-helix	94-102	9
β-strand	104-110	7	3
α-helix	116-120	5
α-helix	121-123	3
α-helix	125-136	12
α-helix	146-156	11
α-helix	161-182	22
α-helix	189-190	2
α-helix	191-200	10
α-helix	201-220	20
α-helix	226-239	14
α-helix	245-249	5
α-helix	250-254	5
β-strand	255-258	4	4
β-strand	261-264	4	4
α-helix	271-290	20
α-helix	294-296	3
α-helix	305-307	3
α-helix	314-328	15
α-helix	330-334	5
α-helix	340-366	27
α-helix	369-406	38

Chain C: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	15-26	12
β-strand	30-34	5	5
β-strand	37-42	6	5
β-strand	45-50	6	5
α-helix	52-61	10
α-helix	67-75	9
α-helix	77-80	4
β-strand	86-87	2	6
α-helix	89-100	12
α-helix	101-106	6
α-helix	116-129	14
α-helix	139-143	5
α-helix	146-165	20
β-strand	179-183	5	6
β-strand	186-191	6	6
β-strand	197-202	6	6
α-helix	205-209	5
β-strand	218-222	5	6
α-helix	224-229	6

Chain D: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	7
β-strand	37-42	6	7
β-strand	45-50	6	7
α-helix	54-60	7
α-helix	67-81	15
β-strand	87	1	8
α-helix	91-101	11
α-helix	102-109	8
α-helix	115-127	13
α-helix	139-143	5
α-helix	146-165	20
α-helix	168-170	3
β-strand	178-182	5	9
β-strand	187-193	7	9
β-strand	196-202	7	9
α-helix	207-210	4
β-strand	218	1	9
β-strand	219	1	8
α-helix	224-229	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoprotein	A, B	protein	739	Zaire ebolavirus	P18272 (AlphaFold model)
Membrane-associated protein VP24	C, D	protein	251	Zaire ebolavirus	Q05322 (AlphaFold model)
RNA (12-mer)	K	RNA	12	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>8Y9J_1 Nucleoprotein (chains A, B)
MDSRPQKIWMAPSLTESDMDYHKILTAGLSVQQGIVRQRVIPVYQVNNLEEICQLIIQAF
EAGVDFQESADSFLLMLCLHHAYQGDYKLFLESGAVKYLEGHGFRFEVKKRDGVKRLEEL
LPAVSSGKNIKRTLAAMPEEETTEANAGQFLSFASLFLPKLVVGEKACLEKVQRQIQVHA
EQGLIQYPTAWQSVGHMMVIFRLMRTNFLIKFLLIHQGMHMVAGHDANDAVISNSVAQAR
FSGLLIVKTVLDHILQKTERGVRLHPLARTAKVKNEVNSFKAALSSLAKHGEYAPFARLL
NLSGVNNLEHGLFPQLSAIALGVATAHGSTLAGVNVGEQYQQLREAATEAEKQLQQYAES
RELDHLGLDDQEKKILMNFHQKKNEISFQQTNAMVTLRKERLAKLTEAITAASLPKTSGH
YDDDDDIPFPGPINDDDNPGHQDDDPTDSQDTTIPDVVVDPDDGSYGEYQSYSENGMNAP
DDLVLFDLDEDDEDTKPVPNRSTKGGQQKNSQKGQHIEGRQTQSRPIQNVPGPHRTIHHA
SAPLTDNDRRNEPSGSTSPRMLTPINEEADPLDDADDETSSLPPLESDDEEQDRDGTSNR
TPTVAPPAPVYRDHSEKKELPQDEQQDQDHTQEARNQDSDNTQSEHSFEEMYRHILRSQG
PFDAVLYYHMMKDEPVVFSTSDGKEYTYPDSLEEEYPPWLTEKEAMNEENRFVTLDGQQF
YWPVMNHKNKFMAILQHHQ

Sequence of entity 2 (C, D), FASTA

>8Y9J_2 Membrane-associated protein VP24 (chains C, D)
MAKATGRYNLISPKKDLEKGVVLSDLCNFLVSQTIQGWKVYWAGIEFDVTHKGMALLHRL
KTNDFAPAWSMTRNLFPHLFQNPNSTIESPLWALRVILAAGIQDQLIDQSLIEPLAGALG
LISDWLLTTNTNHFNMRTQRVKEQLSLKMLSLIRSNILKFINKLDALHVVNYNGLLSSIE
IGTQNHTIIITRTNMGFLVELQEPDKSAMNRMKPGPAKFSLLHESTLKAFTQGSSTRMQS
LILEFNSSLAI

Sequence of entity 3 (K), FASTA

>8Y9J_3 RNA (12-MER) (chains K)
UUUUUUUUUUUU

Primary citation

Structural basis for Ebola virus nucleocapsid assembly and function regulated by VP24. Fujita-Fujiharu, Y., Hu, S., Hirabayashi, A. et al. Nat Commun (2025) 16:2171-2171. DOI 10.1038/s41467-025-57236-4 · PubMed

Other PDB entries of the same protein (UniProt P18272 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QB0 1.75 Å, The crystal structure of the C-terminal domain of Ebola (Zaire) nucleoprotein
4Z9P 1.79 Å, Crystal structure of Ebola virus nucleoprotein core domain at 1.8A resolution
4QAZ 1.98 Å, The crystal structure of the C-terminal domain of Ebola (Zaire) nucleoprotein
5T3T 2.2 Å, Ebola virus VP30 CTD bound to nucleoprotein
4ZTA 2.4 Å, Ebola virus nucleoprotein bound to VP35 chaperoning peptide I212121
4ZTI 2.4 Å, Ebola virus nucleoprotein bound to VP35 chaperoning peptide P212121
4ZTG 2.8 Å, Ebola virus nucleoprotein bound to VP35 chaperoning peptide P22121
6NUT 3.1 Å, Ebola virus nucleoprotein - RNA complex
5Z9W 3.6 Å, Ebola virus nucleoprotein-RNA complex
4YPI 3.71 Å, Structure of Ebola virus nucleoprotein N-terminal fragment bound to a peptide derived…
6C54 5.8 Å, Ebola nucleoprotein nucleocapsid-like assembly and the asymmetric unit
6EHL 6.6 Å, Model of the Ebola virus nucleoprotein in recombinant nucleocapsid-like assemblies

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