8USN: Nucleoprotein

Intracellular cryo-tomography structure of EBOV nucleocapsid at 8.9 Angstrom. Determined by electron microscopy at 8.9 Å resolution. Released 2 Oct 2024.

Method: Electron microscopy
Resolution: 8.9 Å
Organisms: Ebola virus - Mayinga, Zaire, 1976, Zaire
Chains: 9
Atoms: 6,954
Mol. weight: 385.33 kDa
Released: 2 Oct 2024

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

Secondary structure: helices and β-sheets

8USN contains 101 α-helices and 34 β-strands across 7 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.

Chains A and B: 24 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
β-strand	39-45	7	1
α-helix	49-60	12
α-helix	67-82	16
α-helix	87-90	4
α-helix	94-100	7
β-strand	104-110	7	1
α-helix	117-120	4
α-helix	128-135	8
α-helix	147-155	9
α-helix	165-181	17
α-helix	189-192	4
α-helix	194-206	13
α-helix	208-220	13
α-helix	227-238	12
α-helix	245-248	4
α-helix	249-254	6
β-strand	255-258	4	2
β-strand	261-264	4	2
α-helix	271-287	17
α-helix	288-296	9
α-helix	297-300	4
α-helix	306-308	3
α-helix	310-312	3
α-helix	314-327	14
α-helix	338-362	25
α-helix	363-365	3
α-helix	370-405	36

Chain E: 23 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	38	1
β-strand	39-45	7	5
α-helix	49-62	14
α-helix	72-82	11
α-helix	87-91	5
α-helix	94-100	7
β-strand	104-110	7	5
α-helix	117-120	4
α-helix	125-135	11
α-helix	147-154	8
α-helix	155-157	3
α-helix	165-181	17
α-helix	184-188	5
α-helix	194-206	13
α-helix	209-219	11
α-helix	221-223	3
α-helix	227-237	11
α-helix	245-254	10
β-strand	255-258	4	6
β-strand	261-264	4	6
α-helix	267-269	3
α-helix	271-288	18
α-helix	291-293	3
α-helix	305-308	4
α-helix	310-312	3
α-helix	314-327	14
α-helix	341-352	12

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	28-34	7

Chains I and J: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	22-27	6
β-strand	30-34	5	7
β-strand	37-42	6	7
β-strand	45-49	5	7
α-helix	54-61	8
α-helix	67-75	9
β-strand	86-87	2	8
α-helix	90-107	18
α-helix	113-127	15
α-helix	140-144	5
α-helix	147-165	19
α-helix	167-168	2
β-strand	169	1	8
α-helix	170	1
β-strand	179-182	4	8
β-strand	187-193	7	8
β-strand	196-201	6	8
β-strand	218-222	5	8
α-helix	224-230	7

Chain K: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	222-231	10
α-helix	238-253	16
α-helix	256-268	13
α-helix	273-281	9
α-helix	291-293	3
β-strand	294-297	4	11
α-helix	305-308	4
β-strand	311-312	2	11
α-helix	320-322	3
β-strand	324-330	7	11
β-strand	334-339	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoprotein	A, B, E	protein	739	Ebola virus - Mayinga, Zaire, 1976	P18272 (AlphaFold model)
RNA (5'-r(apapapapapa)-3')	C, D	RNA	6	Zaire
Membrane-associated protein VP24	I, J	protein	251	Ebola virus - Mayinga, Zaire, 1976	Q05322 (AlphaFold model)
Polymerase cofactor VP35	F, K	protein	340	Ebola virus - Mayinga, Zaire, 1976	Q05127 (AlphaFold model)

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

>8USN_1 Nucleoprotein (chains A, B, E)
MDSRPQKIWMAPSLTESDMDYHKILTAGLSVQQGIVRQRVIPVYQVNNLEEICQLIIQAF
EAGVDFQESADSFLLMLCLHHAYQGDYKLFLESGAVKYLEGHGFRFEVKKRDGVKRLEEL
LPAVSSGKNIKRTLAAMPEEETTEANAGQFLSFASLFLPKLVVGEKACLEKVQRQIQVHA
EQGLIQYPTAWQSVGHMMVIFRLMRTNFLIKFLLIHQGMHMVAGHDANDAVISNSVAQAR
FSGLLIVKTVLDHILQKTERGVRLHPLARTAKVKNEVNSFKAALSSLAKHGEYAPFARLL
NLSGVNNLEHGLFPQLSAIALGVATAHGSTLAGVNVGEQYQQLREAATEAEKQLQQYAES
RELDHLGLDDQEKKILMNFHQKKNEISFQQTNAMVTLRKERLAKLTEAITAASLPKTSGH
YDDDDDIPFPGPINDDDNPGHQDDDPTDSQDTTIPDVVVDPDDGSYGEYQSYSENGMNAP
DDLVLFDLDEDDEDTKPVPNRSTKGGQQKNSQKGQHIEGRQTQSRPIQNVPGPHRTIHHA
SAPLTDNDRRNEPSGSTSPRMLTPINEEADPLDDADDETSSLPPLESDDEEQDRDGTSNR
TPTVAPPAPVYRDHSEKKELPQDEQQDQDHTQEARNQDSDNTQSEHSFEEMYRHILRSQG
PFDAVLYYHMMKDEPVVFSTSDGKEYTYPDSLEEEYPPWLTEKEAMNEENRFVTLDGQQF
YWPVMNHKNKFMAILQHHQ

Sequence of entity 2 (C, D), FASTA

>8USN_2 RNA (5'-R(*AP*AP*AP*AP*AP*A)-3') (chains C, D)
AAAAAA

Sequence of entity 3 (I, J), FASTA

>8USN_3 Membrane-associated protein VP24 (chains I, J)
MAKATGRYNLISPKKDLEKGVVLSDLCNFLVSQTIQGWKVYWAGIEFDVTHKGMALLHRL
KTNDFAPAWSMTRNLFPHLFQNPNSTIESPLWALRVILAAGIQDQLIDQSLIEPLAGALG
LISDWLLTTNTNHFNMRTQRVKEQLSLKMLSLIRSNILKFINKLDALHVVNYNGLLSSIE
IGTQNHTIIITRTNMGFLVELQEPDKSAMNRMKPGPAKFSLLHESTLKAFTQGSSTRMQS
LILEFNSSLAI

Sequence of entity 4 (F, K), FASTA

>8USN_4 Polymerase cofactor VP35 (chains F, K)
MTTRTKGRGHTAATTQNDRMPGPELSGWISEQLMTGRIPVSDIFCDIENNPGLCYASQMQ
QTKPNPKTRNSQTQTDPICNHSFEEVVQTLASLATVVQQQTIASESLEQRITSLENGLKP
VYDMAKTISSLNRVCAEMVAKYDLLVMTTGRATATAAATEAYWAEHGQPPPGPSLYEESA
IRGKIESRDETVPQSVREAFNNLNSTTSLTEENFGKPDISAKDLRNIMYDHLPGFGTAFH
QLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSR
GDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI

Primary citation

Intracellular Ebola virus nucleocapsid assembly revealed by in situ cryo-electron tomography. Watanabe, R., Zyla, D., Parekh, D. et al. Cell (2024) 187:5587-5603.e19. DOI 10.1016/j.cell.2024.08.044 · 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…
8Y9J 4.6 Å, Structure of the Ebola virus nucleocapsid subunit
6C54 5.8 Å, Ebola nucleoprotein nucleocapsid-like assembly and the asymmetric unit

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