4WYK: LRR and NTF2-like domains of NXF1

Structure of the LRR and NTF2-like domains of NXF1 complexed with NXT1. Determined by X-ray diffraction at 3.4 Å resolution. Released 4 Feb 2015.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,679
Mol. weight: 135.63 kDa
Released: 4 Feb 2015

Explore 4WYK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WYK contains 51 α-helices and 44 β-strands across 4 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: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	206-219	14
β-strand	220-221	2	1
β-strand	226-228	3	1
α-helix	236-240	5
α-helix	250-263	14
β-strand	269-271	3	1
α-helix	281-283	3
α-helix	286-289	4
β-strand	295-297	3	1
α-helix	306-312	7
β-strand	319-321	3	1
α-helix	326-329	4
α-helix	334-344	11
β-strand	350-351	2	1
β-strand	354-355	2	1
α-helix	357-359	3
α-helix	369-373	5
β-strand	377	1	2
α-helix	381-399	19
α-helix	403-408	6
β-strand	410-419	10	2
α-helix	433-436	4
α-helix	448-454	7
β-strand	456	1	2
α-helix	459-468	10
α-helix	470-471	2
β-strand	472-474	3	2
α-helix	476-478	3
β-strand	480-486	7	2
β-strand	491-501	11	2
β-strand	510-522	13	2
α-helix	523-525	3
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	6-30	25
α-helix	32-35	4
α-helix	36-38	3
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	82-84	3
β-strand	90-101	12	3
β-strand	107-119	13	3
β-strand	124-135	12	3

Chain C: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	203-205	3
α-helix	206-219	14
β-strand	220-221	2	4
β-strand	226-228	3	4
α-helix	236-240	5
α-helix	250-263	14
β-strand	269-271	3	4
α-helix	281-283	3
α-helix	286-289	4
β-strand	295-297	3	4
α-helix	306-312	7
β-strand	319-321	3	4
α-helix	326-329	4
α-helix	334-344	11
β-strand	350-351	2	4
β-strand	354-355	2	4
α-helix	358-359	2
α-helix	369-373	5
β-strand	377	1	5
α-helix	381-400	20
α-helix	403-408	6
β-strand	410-419	10	5
α-helix	431-437	7
α-helix	448-454	7
β-strand	456	1	5
α-helix	459-468	10
α-helix	470-471	2
β-strand	472-474	3	5
β-strand	480-486	7	5
β-strand	491-501	11	5
α-helix	506-508	3
β-strand	510-521	12	5
β-strand	527-538	12	5
α-helix	539-540	2
α-helix	541-545	5

Chain D: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-30	25
α-helix	32-35	4
α-helix	36-38	3
β-strand	39-47	9	6
β-strand	50-53	4	6
α-helix	55-64	10
α-helix	66-67	2
β-strand	68	1	7
β-strand	71-79	9	6
β-strand	90-99	10	6
β-strand	101	1	7
β-strand	107-119	13	6
β-strand	124-135	12	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear RNA export factor 1	A, C	protein	461	Homo sapiens	Q9UBU9 (AlphaFold model)
NTF2-related export protein 1	B, D	protein	139	Homo sapiens	Q9UKK6 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4WYK_1 Nuclear RNA export factor 1 (chains A, C)
SVRRDRAPPERGGAGTSQDGTSKNWFKITIPYGRKYDKAWLLSMIQSKCSVPFTPIEFHY
ENTRAQFFVEDASTASALKAVNYKILDRENRRISIIINSSAPPHTILNELKPEQVEQLKL
IMSKRYDGSQQALDLKGLRSDPDLVAQNIDVVLNRRSCMAATLRIIEENIPELLSLNLSN
NRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLCDTFRDQ
STYISAIRERFPKLLRLDGHELPPPIAFDVEAPTTLPPCKGSYFGTENLKSLVLHFLQQY
YAIYDSGDRQGLLDAYHDGACCSLSIPFIPQNPARSSLAEYFKDSRNVKKLKDPTLRFRL
LKHTRLNVVAFLNELPKTQHDVNSFVVDISAQTSTLLCFSVNGVFKEVDGKSRDSLRAFT
RTFIAVPASNSGLCIVNDELFVRNASSEEIQRAFAMPAPTP

Sequence of entity 2 (B, D), FASTA

>4WYK_2 NTF2-related export protein 1 (chains B, D)
ASVDFKTYVDQACRAAEEFVNVYYTTMDKRRRLLSRLYMGTATLVWNGNAVSGQESLSEF
FEMLPSSEFQISVVDCQPVHDEATPSQTTVLVVICGSVKFEGNKQRDFNQNFILTAQASP
SNTVWKIASDCFRFQDWAS

Primary citation

The principal mRNA nuclear export factor NXF1:NXT1 forms a symmetric binding platform that facilitates export of retroviral CTE-RNA. Aibara, S., Katahira, J., Valkov, E. et al. Nucleic Acids Res (2015) 43:1883-1893. DOI 10.1093/nar/gkv032 · 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
1KOH 3.8 Å, The crystal structure and mutational analysis of a novel RNA-binding domain found in the…
1KOO 3.8 Å, The crystal structure and mutational analysis of a novel RNA-binding domain found in the…

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