6E5U: MRNA export receptor NXF1/NXT1

Crystal structure of the mRNA export receptor NXF1/NXT1 in complex with influenza virus NS1 protein. Determined by X-ray diffraction at 3.8 Å resolution. Released 24 Apr 2019.

Method: X-ray diffraction
Resolution: 3.8 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 16
Atoms: 20,434
Mol. weight: 395.81 kDa
Released: 24 Apr 2019

Explore 6E5U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E5U contains 113 α-helices and 114 β-strands across 16 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: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	206-218	13
β-strand	220-221	2	1
β-strand	226-228	3	1
α-helix	235-237	3
α-helix	250-263	14
β-strand	269-271	3	1
α-helix	284-286	3
β-strand	295-297	3	1
α-helix	306-311	6
β-strand	319-321	3	1
α-helix	326-330	5
α-helix	334-344	11
β-strand	350-351	2	1
β-strand	354-355	2	1
α-helix	356-358	3
α-helix	369-372	4
β-strand	377	1	2
α-helix	381-398	18
α-helix	403-408	6
β-strand	410-419	10	2
α-helix	433-438	6
β-strand	439	1	2
α-helix	448-453	6
β-strand	456	1	2
α-helix	459-467	9
α-helix	470-471	2
β-strand	472-486	15	2
β-strand	491-501	11	2
β-strand	510-522	13	2
β-strand	526-538	13	2
α-helix	539-540	2
α-helix	541-545	5

Chain B: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
α-helix	32-38	7
β-strand	39-47	9	3
β-strand	50-53	4	3
α-helix	55-64	10
α-helix	66-67	2
β-strand	68-79	12	3
α-helix	80-81	2
β-strand	90-101	12	3
β-strand	104-118	15	3
α-helix	119	1
β-strand	125-135	11	3

Chain C: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	206-218	13
β-strand	220-221	2	4
β-strand	226-227	2	4
β-strand	228	1	5
α-helix	240-242	3
α-helix	250-263	14
β-strand	269	1	6
β-strand	271	1	5
α-helix	284-286	3
β-strand	295-297	3	6
α-helix	306-311	6
β-strand	319-321	3	6
α-helix	326-330	5
α-helix	334-342	9
β-strand	350-351	2	6
β-strand	354-355	2	6
α-helix	356-358	3
α-helix	369-372	4
β-strand	377	1	7
α-helix	381-398	18
α-helix	403-408	6
β-strand	410-419	10	7
α-helix	433-436	4
α-helix	448-453	6
β-strand	456	1	7
α-helix	459-467	9
α-helix	470-471	2
β-strand	472-474	3	7
α-helix	476-478	3
β-strand	480-486	7	7
β-strand	491-501	11	7
β-strand	510-522	13	7
β-strand	526-538	13	7
α-helix	539-540	2
α-helix	541-545	5

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
α-helix	32-38	7
β-strand	39-47	9	8
β-strand	50-53	4	8
α-helix	55-64	10
α-helix	66-67	2
β-strand	68-79	12	8
β-strand	89-101	13	8
β-strand	104-118	15	8
α-helix	119	1
β-strand	125-135	11	8

Chain E: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	206-218	13
β-strand	220-221	2	9
β-strand	226-228	3	9
α-helix	238-241	4
α-helix	250-263	14
β-strand	269-271	3	9
α-helix	284-286	3
β-strand	295-297	3	9
α-helix	306-311	6
β-strand	319-321	3	9
α-helix	326-330	5
α-helix	334-342	9
β-strand	350-351	2	9
β-strand	354-355	2	9
α-helix	356-358	3
α-helix	369-372	4
β-strand	377	1	10
α-helix	381-398	18
α-helix	403-408	6
β-strand	410-419	10	10
α-helix	436-438	3
β-strand	439	1	10
α-helix	448-453	6
β-strand	456	1	10
α-helix	459-467	9
α-helix	470-471	2
β-strand	472-474	3	10
β-strand	480-486	7	10
β-strand	491-501	11	10
β-strand	510-522	13	10
β-strand	526-538	13	10
α-helix	539-540	2
α-helix	541-545	5

Chain F: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-30	25
α-helix	32-38	7
β-strand	39-47	9	11
β-strand	50-53	4	11
α-helix	55-64	10
α-helix	66-67	2
β-strand	68-79	12	11
β-strand	90-101	12	11
β-strand	104-118	15	11
α-helix	119	1
β-strand	125-135	11	11

Chain G: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	206-218	13
β-strand	220-221	2	12
β-strand	226-228	3	12
α-helix	236-239	4
α-helix	250-263	14
β-strand	269-271	3	12
α-helix	284-286	3
β-strand	295-297	3	12
α-helix	306-311	6
β-strand	319-321	3	12
α-helix	326-330	5
α-helix	334-342	9
β-strand	350-351	2	12
β-strand	354-355	2	12
α-helix	356-358	3
α-helix	369-372	4
β-strand	377	1	13
α-helix	381-398	18
α-helix	403-408	6
β-strand	410-419	10	13
α-helix	433-438	6
β-strand	439	1	13
α-helix	448-453	6
β-strand	456	1	13
α-helix	459-467	9
α-helix	470-471	2
β-strand	472-474	3	13
β-strand	480-486	7	13
β-strand	491-501	11	13
β-strand	510-522	13	13
β-strand	526-538	13	13
α-helix	539-540	2
α-helix	541-545	5

Chain H: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
α-helix	32-38	7
β-strand	39-47	9	14
β-strand	50-53	4	14
α-helix	55-64	10
α-helix	66-67	2
β-strand	68-80	13	14
β-strand	90-101	12	14
β-strand	107-118	12	14
α-helix	119	1
β-strand	125-135	11	14

7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear RNA export factor 1	A, C, E, G	protein	508	Homo sapiens	Q9UBU9 (AlphaFold model)
NTF2-related export protein 1	B, D, F, H	protein	140	Homo sapiens	Q9UKK6 (AlphaFold model)
Non-structural protein 1	J, K, L, M	protein	77	Influenza A virus	I7CAR2
Non-structural protein 1	U, V, X, Y	protein	153	Influenza A virus	I7CAR2

Sequence of entity 1 (A, C, E, G), FASTA

>6E5U_1 Nuclear RNA export factor 1 (chains A, C, E, G)
GAMGSKNWFKITIPYGRKYDKAWLLSMIQSKCSVPFTPIEFHYENTRAQFFVEDASTASA
LKAVNYKILDRENRRISIIINSSAPPHTILNELKPEQVEQLKLIMSKRYDGSQQALDLKG
LRSDPDLVAQNIDVVLNRRSCMAATLRIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAP
NLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLCDTFRDQSTYISAIRERFPKLLRL
DGHELPPPIAFDVEAPTTLPPCKGSYFGTENLKSLVLHFLQQYYAIYDSGDRQGLLDAYH
DGACCSLSIPFIPQNPARSSLAEYFKDSRNVKKLKDPTLRFRLLKHTRLNVVAFLNELPK
TQHDVNSFVVDISAQTSTLLCFSVNGVFKEVDGKSRDSLRAFTRTFIAVPASNSGLCIVN
DELFVRNASSEEIQRAFAMPAPTPSSSPVPTLSPEQQEMLQAFSTQSGMNLEWSQKCLQD
NNWDYTRSAQAFTHLKAKGEIPEVAFMK

Sequence of entity 2 (B, D, F, H), FASTA

>6E5U_2 NTF2-related export protein 1 (chains B, D, F, H)
MASVDFKTYVDQACRAAEEFVNVYYTTMDKRRRLLSRLYMGTATLVWNGNAVSGQESLSE
FFEMLPSSEFQISVVDCQPVHDEATPSQTTVLVVICGSVKFEGNKQRDFNQNFILTAQAS
PSNTVWKIASDCFRFQDWAS

Sequence of entity 3 (J, K, L, M), FASTA

>6E5U_3 Non-structural protein 1 (chains J, K, L, M)
GAMGSMDSNTVSSFQVDCFLWHVRKQVADQELGDAPFLDRLRADQASLKGRGSTLGLNIE
TATCVGKQIVERILKEE

Sequence of entity 4 (U, V, X, Y), FASTA

>6E5U_4 Non-structural protein 1 (chains U, V, X, Y)
SDEAFKMPASRYLTDMTIEEMSRDWFMLMPKQKVAGPLCVRMDQAIMDKNIILKANFSVI
FDRLETLTLLRAFTEEGAIVGEISPLPSLPGHTNEDVKNAIGVLIGGLEWNDNTVRVSET
LQRFAWRSSNENGGPPLTPTQKRKMAGTIRSEV

Primary citation

Structural basis for influenza virus NS1 protein block of mRNA nuclear export. Zhang, K., Xie, Y., Munoz-Moreno, R. et al. Nat Microbiol (2019) 4:1671-1679. DOI 10.1038/s41564-019-0482-x · PubMed

Other PDB entries of the same protein (UniProt Q9UBU9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1OAI 1.0 Å, Complex between Tap UBA domain and FxFG nucleoporin peptide
9I8A 1.5 Å, NXT1-NXF1 complex crystallized in space group P65 2 2
1JKG 1.9 Å, Structural basis for the recognition of a nucleoporin FG-repeat by the NTF2-like domain…
3RW6 2.3 Å, Structure of nuclear RNA export factor TAP bound to CTE RNA
2Z5K 2.6 Å, Complex of Transportin 1 with TAP NLS
1JN5 2.8 Å, Structural basis for the recognition of a nucleoporin FG-repeat by the NTF2-like domain…
1FO1 2.9 Å, Crystal structure of the RNA-binding domain of the mRNA export factor tap
2Z5M 3.0 Å, Complex of Transportin 1 with TAP NLS, crystal form 2
3RW7 3.0 Å, Structure of N-terminal domain of nuclear RNA export factor TAP
1FT8 3.15 Å, Crystal structure of the RNA-binding domain of the mRNA export factor tap
4WYK 3.4 Å, Structure of the LRR and NTF2-like domains of NXF1 complexed with NXT1
1KOH 3.8 Å, The crystal structure and mutational analysis of a novel RNA-binding domain found in the…

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