5NT1: E3 ubiquitin/ISG15 ligase TRIM25

Name: PDB 5NT1: Complex of influenza A NS1 effector domain with TRIM25 coiled coil
Published: 2018-05-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Complex of influenza A NS1 effector domain with TRIM25 coiled coil. Determined by X-ray diffraction at 2.82 Å resolution. Released 16 May 2018.

Method: X-ray diffraction
Resolution: 2.82 Å
Organisms: Homo sapiens, Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Chains: 6
Atoms: 7,038
Mol. weight: 117.29 kDa
Released: 16 May 2018

Explore 5NT1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NT1 contains 19 α-helices and 21 β-strands across 6 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 E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	191-298	108
α-helix	307-311	5
α-helix	331-356	26

Chains B, F and J: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	87-91	5	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	140-151	12	1
β-strand	156-162	7	1
α-helix	171-186	16
β-strand	191-194	4	1
α-helix	196-202	7

Chain I: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	191-298	108
α-helix	307-311	5
α-helix	325-327	3
α-helix	331-356	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin/ISG15 ligase TRIM25	A, E, I	protein	193	Homo sapiens	Q14258 (AlphaFold model)
Non-structural protein 1	B, F, J	protein	154	Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)	P03496 (AlphaFold model)

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

>5NT1_1 E3 ubiquitin/ISG15 ligase TRIM25 (chains A, E, I)
GPGSLSQASADLEATLRHKLTVMYSQINGASRALDDVRNRQQDVRMTANRKVEQLQQEYT
EMKALLDASETTSTRKIKEEEKRVNSKFDTIYQILLKKKSEIQTLKEEIEQSLTKRDEFE
FLEKASKLRGISTKPVYIPEVELNHKLIKGIHQSTIDLKNELKQCIGRLQELTPSSGDPG
EHDPASTHKSTRP

Sequence of entity 2 (B, F, J), FASTA

>5NT1_2 Non-structural protein 1 (chains B, F, J)
GPGTMASVPASRYLTDMTLEEMSREWSMLIPKQKVAGPLCIRMDQAIMDKNIILKANFSV
IFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTAEDVKNAVGVLIGGLEWNDNTVRVSE
TLQRFAWRSSNENGRPPLTPKQKREMAGTIRSEV

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 Q14258 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9I0T 1.8 Å, Crystal structure of TRIM25 PRYSPRY covalently bound to…
6FLM 2.01 Å, Crystal structure of the human TRIM25 PRYSPRY domain
5FER 2.34 Å, Complex of TRIM25 RING with UbcH5-Ub
5EYA 2.4 Å, TRIM25 RING domain in complex with Ubc13-Ub conjugate
4LTB 2.59 Å, Coiled-coil domain of TRIM25
9IUN 2.7 Å, Crystal structure of Trim25 Pspry
4CFG 2.8 Å, Structure of the TRIM25 coiled-coil
6FLN 3.6 Å, Crystal structure of the human TRIM25 coiled-coil and PRYSPRY domains
5NT2 4.26 Å, Complex of influenza A NS1 with TRIM25 coiled coil domain

Browse structure collections

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