5NT2: Non-structural protein 1

Complex of influenza A NS1 with TRIM25 coiled coil domain. Determined by X-ray diffraction at 4.26 Å resolution. Released 23 May 2018.

Method: X-ray diffraction
Resolution: 4.26 Å
Organisms: Influenza A virus (strain A/Puerto Rico/8/1934 H1N1), Homo sapiens
Chains: 8
Atoms: 10,516
Mol. weight: 191.52 kDa
Released: 23 May 2018

Explore 5NT2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NT2 contains 30 α-helices and 32 β-strands across 8 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 N: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	191-296	106
α-helix	306-311	6
α-helix	331-356	26

Chain C: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	88-91	4	3
α-helix	95-98	4
β-strand	107-112	6	3
β-strand	115-120	6	3
β-strand	127-137	11	3
β-strand	140-150	11	3
β-strand	156-162	7	3
β-strand	163	1	4
β-strand	166	1	4
α-helix	171-186	16
β-strand	191-194	4	3
α-helix	196-200	5

Chain D: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
α-helix	30-50	21
α-helix	54-64	11
β-strand	87-91	5	5
α-helix	95-99	5
β-strand	107-112	6	5
β-strand	115-120	6	5
β-strand	127-137	11	5
β-strand	140-150	11	5
β-strand	156-162	7	5
α-helix	171-186	16
β-strand	191-194	4	5
α-helix	196-200	5

Chain E: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
α-helix	30-50	21
α-helix	54-65	12
β-strand	88-91	4	6
α-helix	95-99	5
β-strand	107-112	6	6
β-strand	115-120	6	6
β-strand	127-137	11	6
β-strand	140-150	11	6
β-strand	156-162	7	6
α-helix	171-186	16
β-strand	191-194	4	6
α-helix	196-200	5

Chain F: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	88-91	4	1
α-helix	95-99	5
β-strand	107-112	6	1
β-strand	115-120	6	1
β-strand	127-137	11	1
β-strand	140-150	11	1
β-strand	156-162	7	1
β-strand	163	1	2
β-strand	166	1	2
α-helix	171-186	16
β-strand	191-194	4	1
α-helix	196-200	5

Chain I: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	191-298	108
α-helix	305-311	7
α-helix	331-356	26

Chain V: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	191-298	108
α-helix	306-316	11
α-helix	331-356	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-structural protein 1	C, D, E, F	protein	233	Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)	P03496 (AlphaFold model)
E3 ubiquitin/ISG15 ligase TRIM25	A, I, N, V	protein	193	Homo sapiens	Q14258 (AlphaFold model)

Sequence of entity 1 (C, D, E, F), FASTA

>5NT2_1 Non-structural protein 1 (chains C, D, E, F)
GPGMDPNTVSSFQVDCFLWHVRKRVADQELGDAPFLDRLRADQASLRGRGSTLGLDIETA
TRAGKQIVERILKEESDEALKMTMASVPASRYLTDMTLEEMSREWSMLIPKQKVAGPLCI
RMDQAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTAEDVKNA
VGVLIGGLEANDNTVRVSETLQRFAWRSSNENGRPPLTPKQKREMAGTIRSEV

Sequence of entity 2 (A, I, N, V), FASTA

>5NT2_2 E3 ubiquitin/ISG15 ligase TRIM25 (chains A, I, N, V)
GPGSLSQASADLEATLRHKLTVMYSQINGASRALDDVRNRQQDVRMTANRKVEQLQQEYT
EMKALLDASETTSTRKIKEEEKRVNSKFDTIYQILLKKKSEIQTLKEEIEQSLTKRDEFE
FLEKASKLRGISTKPVYIPEVELNHKLIKGIHQSTIDLKNELKQCIGRLQELTPSSGDPG
EHDPASTHKSTRP

Primary citation

Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition. Koliopoulos, M.G., Lethier, M., van der Veen, A.G. et al. Nat Commun (2018) 9:1820-1820. DOI 10.1038/s41467-018-04214-8 · PubMed

Other PDB entries of the same protein (UniProt P03496 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ZKO 1.7 Å, Structural basis for dsRNA recognition by NS1 protein of human influenza virus A
3RVC 1.8 Å, Effector domain of NS1 from influenza A/PR/8/34 containing a W187A mutation
3O9R 2.0 Å, Effector domain of NS1 from influenza A/PR/8/34 containing a W187A mutation
2GX9 2.1 Å, X-ray structure of influenza virus NS1 effector domain
3O9T 2.2 Å, Effector domain from influenza A/PR/8/34 NS1
3L4Q 2.3 Å, Structural insights into phosphoinositide 3-kinase activation by the influenza A virus…
3O9S 2.48 Å, Effector domain of influenza A/PR/8/34 NS1
3O9Q 2.5 Å, Effector domain of NS1 from A/PR/8/34 containing a W187A mutation
5NT1 2.82 Å, Complex of influenza A NS1 effector domain with TRIM25 coiled coil
3O9U 3.2 Å, Effector domain of influenza A/PR/8/34 NS1

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