6NUT: Ebola virus nucleoprotein - RNA complex

Ebola virus nucleoprotein - RNA complex. Determined by electron microscopy at 3.1 Å resolution. Released 1 May 2019.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Zaire ebolavirus (strain Mayinga-76), Homo sapiens
Chains: 2
Atoms: 3,123
Mol. weight: 52.2 kDa
Released: 1 May 2019

Explore 6NUT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NUT contains 28 α-helices and 4 β-strands across 1 chain. 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: 28 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
β-strand	39-44	6	1
α-helix	49-61	13
α-helix	67-69	3
α-helix	70-83	14
α-helix	87-90	4
α-helix	94-100	7
β-strand	104-109	6	1
α-helix	117-119	3
α-helix	128-135	8
α-helix	147-155	9
α-helix	161-163	3
α-helix	165-182	18
α-helix	189-192	4
α-helix	194-206	13
α-helix	208-220	13
α-helix	227-237	11
α-helix	246-249	4
α-helix	250-254	5
β-strand	255-258	4	2
β-strand	261-264	4	2
α-helix	265	1
α-helix	266-268	3
α-helix	271-287	17
α-helix	288-296	9
α-helix	305-307	3
α-helix	310-312	3
α-helix	314-324	11
α-helix	331-333	3
α-helix	338-362	25
α-helix	363-365	3
α-helix	371-405	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoprotein	A	protein	450	Zaire ebolavirus (strain Mayinga-76)	P18272 (AlphaFold model)
RNA (5'-r(papapapapapa)-3')	D	RNA	6	Homo sapiens

Sequence of entity 1 (A), FASTA

>6NUT_1 Nucleoprotein (chains A)
MDSRPQKIWMAPSLTESDMDYHKILTAGLSVQQGIVRQRVIPVYQVNNLEEICQLIIQAF
EAGVDFQESADSFLLMLCLHHAYQGDYKLFLESGAVKYLEGHGFRFEVKKRDGVKRLEEL
LPAVSSGKNIKRTLAAMPEEETTEANAGQFLSFASLFLPKLVVGEKACLEKVQRQIQVHA
EQGLIQYPTAWQSVGHMMVIFRLMRTNFLIKFLLIHQGMHMVAGHDANDAVISNSVAQAR
FSGLLIVKTVLDHILQKTERGVRLHPLARTAKVKNEVNSFKAALSSLAKHGEYAPFARLL
NLSGVNNLEHGLFPQLSAIALGVATAHGSTLAGVNVGEQYQQLREAATEAEKQLQQYAES
RELDHLGLDDQEKKILMNFHQKKNEISFQQTNAMVTLRKERLAKLTEAITAASLPKTSGH
YDDDDDIPFPGPINDDDNPGHQDDDPTDSQ

Sequence of entity 2 (D), FASTA

>6NUT_2 RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') (chains D)
AAAAAA

Primary citation

Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex. Kirchdoerfer, R.N., Saphire, E.O., Ward, A.B. Acta Crystallogr F Struct Biol Commun (2019) 75:340-347. DOI 10.1107/S2053230X19004424 · 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
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
6EHL 6.6 Å, Model of the Ebola virus nucleoprotein in recombinant nucleocapsid-like assemblies

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