3TKN: Nup82-Nup159-Nup98 heterotrimer

Structure of the Nup82-Nup159-Nup98 heterotrimer. Determined by X-ray diffraction at 3.4 Å resolution. Released 11 Apr 2012.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Saccharomyces cerevisiae, Mus musculus
Chains: 9
Atoms: 15,021
Mol. weight: 219.13 kDa
Released: 11 Apr 2012

Explore 3TKN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3TKN contains 47 α-helices and 136 β-strands across 9 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: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	25-27	3	1
β-strand	34-39	6	1
β-strand	42-47	6	1
β-strand	55-58	4	1
β-strand	70-73	4	2
β-strand	79-83	5	2
β-strand	87-92	6	2
β-strand	110-115	6	2
α-helix	125-126	2
β-strand	127-132	6	3
β-strand	136	1	4
β-strand	141-146	6	3
β-strand	151-155	5	3
β-strand	164-166	3	3
α-helix	179-180	2
β-strand	182-187	6	5
β-strand	194-198	5	5
β-strand	204-208	5	5
β-strand	215-217	3	4
α-helix	220-235	16
α-helix	243-261	19
β-strand	269-271	3	4
α-helix	274-277	4
α-helix	280-281	2
β-strand	282	1	5
β-strand	286-288	3	6
α-helix	293-295	3
β-strand	299-306	8	6
β-strand	313-319	7	6
β-strand	323-329	7	6
β-strand	342	1	5
β-strand	347-355	9	6
β-strand	362-364	3	7
β-strand	372-376	5	7
β-strand	380-385	6	7
α-helix	390-399	10
α-helix	403-405	3
β-strand	413-419	7	7
β-strand	425-429	5	8
β-strand	436-440	5	8
β-strand	446	1	8
β-strand	449	1	8

Chains B, E and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1435-1457	23

Chains C, F and I: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	735	1	9
β-strand	741-744	4	10
α-helix	749-752	4
β-strand	763-769	7	10
β-strand	773-780	8	10
β-strand	787	1	9
α-helix	788-790	3
β-strand	792-795	4	11
β-strand	798-801	4	11
β-strand	819-823	5	10
β-strand	829	1	12
β-strand	836	1	12
α-helix	840-845	6
α-helix	848-857	10
β-strand	862-867	6	10
β-strand	872-877	6	10

Chain D: 12 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	25-27	3	13
β-strand	34-39	6	13
β-strand	42-47	6	13
β-strand	55-58	4	13
β-strand	70-73	4	14
β-strand	79-83	5	14
β-strand	87-92	6	14
β-strand	110-115	6	14
α-helix	125-126	2
β-strand	127-132	6	15
β-strand	136	1	16
α-helix	137-139	3
β-strand	141-146	6	15
β-strand	151-155	5	15
β-strand	164-166	3	15
β-strand	173-174	2	17
α-helix	179-180	2
β-strand	182-187	6	18
β-strand	194-198	5	18
β-strand	204-208	5	18
β-strand	215-217	3	16
α-helix	220-234	15
α-helix	243-261	19
β-strand	269-271	3	16
α-helix	274-277	4
α-helix	280-281	2
β-strand	282	1	18
β-strand	286-288	3	19
α-helix	293-295	3
β-strand	299-306	8	19
β-strand	313-319	7	19
β-strand	323-329	7	19
β-strand	342	1	18
β-strand	347-355	9	19
β-strand	362-364	3	20
β-strand	372-376	5	20
β-strand	380-385	6	20
α-helix	390-395	6
α-helix	396-400	5
α-helix	403-405	3
β-strand	413-419	7	20
β-strand	425-429	5	21
β-strand	436-440	5	21
β-strand	446	1	21
β-strand	449	1	21

Chain G: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	25-27	3	25
β-strand	34-39	6	25
β-strand	42-47	6	25
β-strand	55-58	4	25
β-strand	70-73	4	26
β-strand	79-83	5	26
β-strand	87-92	6	26
β-strand	110-115	6	26
β-strand	127-132	6	27
β-strand	136	1	28
α-helix	137-139	3
β-strand	141-146	6	27
β-strand	151-155	5	27
β-strand	164-166	3	27
α-helix	179-180	2
β-strand	182-187	6	29
β-strand	194-198	5	29
β-strand	204-208	5	29
β-strand	215-217	3	28
α-helix	220-235	16
α-helix	243-261	19
β-strand	269-271	3	28
α-helix	274-277	4
α-helix	280-281	2
β-strand	282	1	29
β-strand	286-288	3	30
α-helix	293-295	3
β-strand	299-306	8	30
β-strand	313-319	7	30
β-strand	323-329	7	30
β-strand	342	1	29
β-strand	347-355	9	30
β-strand	362-364	3	31
β-strand	372-376	5	31
β-strand	380-385	6	31
α-helix	390-399	10
α-helix	403-405	3
β-strand	413-419	7	31
β-strand	425-429	5	32
β-strand	436-440	5	32
β-strand	446	1	32
β-strand	449	1	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoporin NUP82	A, D, G	protein	452	Saccharomyces cerevisiae	P40368 (AlphaFold model)
Nucleoporin NUP159	B, E, H	protein	39	Saccharomyces cerevisiae	P40477 (AlphaFold model)
Nucleoporin 98	C, F, I	protein	152	Mus musculus	Q6PFD9 (AlphaFold model)

Sequence of entity 1 (A, D, G), FASTA

>3TKN_1 Nucleoporin NUP82 (chains A, D, G)
MSQSSRLSALPIFQASLSASQSPRYIFSSQNGTRIVFIQDNIIRWYNVLTDSLYHSLNFS
RHLVLDDTFHVISSTSGDLLCLFNDNEIFVMEVPWGYSNVEDVSIQDAFQIFHYSIDEEE
VGPKSSIKKVLFHPKSYRDSCIVVLKEDDTITMFDILNSQEKPIVLNKPNNSFGLDARVN
DITDLEFSKDGLTLYCLNTTEGGDIFAFYPFLPSVLLLNEKDLNLILNKSLVMYESLDST
TDVIVKRNVIKQLQFVSKLHENWNSRFGKVDIQKEYRLAKVQGPFTINPFPGELYDYTAT
NIATILIDNGQNEIVCVSFDDGSLILLFKDLEMSMSWDVDNYVYNNSLVLIERVKLQREI
KSLITLPEQLGKLYVISDNIIQQVNFMSWASTLSKSINESDLNPLAGLKFESKLEDIATI
ERIPNLAYINWNDQSNLALMSNKTLTFQNISS

Sequence of entity 2 (B, E, H), FASTA

>3TKN_2 Nucleoporin NUP159 (chains B, E, H)
GPHSSITKDMKGFKVVEVGLAMNTKKQIGDFFKNLNMAK

Sequence of entity 3 (C, F, I), FASTA

>3TKN_3 Nucleoporin 98 (chains C, F, I)
GPHAGIVLTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNL
DDIVHIRRKEVIVYVDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINY
EGRLEAVSRKQGAQFKEYRPETGSWVFKVSHF

Primary citation

Molecular basis for the anchoring of proto-oncoprotein nup98 to the cytoplasmic face of the nuclear pore complex. Stuwe, T., Schada von Borzyskowski, L., Davenport, A.M. et al. J Mol Biol (2012) 419:330-346. DOI 10.1016/j.jmb.2012.03.024 · PubMed

Other PDB entries of the same protein (UniProt P40368 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3PBP 2.6 Å, Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex
7N9F 37.0 Å, Structure of the in situ yeast NPC
8ZZA Integrative structure and functional anatomy of a single spoke of a nuclear pore complex
8ZZB Integrative structure and functional anatomy of three spokes of a nuclear pore complex
8ZZC Integrative structure and functional anatomy of eight spokes of a nuclear pore complex
8ZZK Structure of the S. cerevisiae nuclear pore complex cytoplasmic mRNA export platform,…
9A0F Integrative model of the wild type yeast nuclear pore complex

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