3PBP: Nucleoporin NUP82

Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 26 Oct 2011.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Saccharomyces cerevisiae
Chains: 12
Atoms: 19,653
Mol. weight: 292.08 kDa
Released: 26 Oct 2011

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

Secondary structure: helices and β-sheets

3PBP contains 78 α-helices and 184 β-strands across 12 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 D: 14 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	24-29	6	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
α-helix	103-107	5
β-strand	110-115	6	2
α-helix	116-118	3
α-helix	125-126	2
β-strand	127-132	6	3
β-strand	136	1	4
α-helix	137-139	3
β-strand	141-146	6	3
β-strand	151-155	5	3
β-strand	164-166	3	3
β-strand	172-174	3	5
β-strand	182-187	6	6
β-strand	194-198	5	6
β-strand	204-208	5	6
β-strand	215-217	3	4
α-helix	220-235	16
α-helix	243-262	20
β-strand	264	1	4
β-strand	269-271	3	4
α-helix	274-277	4
β-strand	282	1	6
α-helix	284-285	2
β-strand	286-288	3	7
α-helix	290-291	2
α-helix	293-296	4
β-strand	299-306	8	7
β-strand	313-319	7	7
β-strand	323-329	7	7
α-helix	332-333	2
β-strand	342	1	6
β-strand	347-355	9	7
β-strand	362-364	3	8
β-strand	372-376	5	8
β-strand	380-385	6	8
α-helix	387-399	13
α-helix	403-405	3
β-strand	413-419	7	8
α-helix	424	1
β-strand	425-431	7	9
β-strand	434-440	7	9
β-strand	445-449	5	9

Chains B and E: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	970-973	4	10
α-helix	976-981	6
β-strand	990	1	11
β-strand	994-997	4	10
β-strand	1001-1005	5	10
β-strand	1009	1	11
α-helix	1018-1021	4
β-strand	1024-1027	4	5
β-strand	1030-1033	4	5
α-helix	1041-1042	2
β-strand	1051-1055	5	10
β-strand	1061	1	12
β-strand	1068	1	12
α-helix	1075-1084	10
β-strand	1091-1095	5	10
β-strand	1102-1106	5	10

Chains C and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1436-1454	19

Chain G: 15 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	24-29	6	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
α-helix	103-107	5
β-strand	110-115	6	26
α-helix	116-118	3
α-helix	125-126	2
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
β-strand	172-174	3	29
β-strand	182-187	6	30
β-strand	194-198	5	30
β-strand	204-208	5	30
β-strand	215-217	3	28
α-helix	220-235	16
α-helix	243-262	20
β-strand	264	1	28
β-strand	269-271	3	28
α-helix	274-277	4
β-strand	282	1	30
α-helix	284-285	2
β-strand	286-288	3	31
α-helix	290-291	2
α-helix	293-296	4
β-strand	299-306	8	31
β-strand	313-319	7	31
β-strand	323-328	6	31
α-helix	332-333	2
β-strand	342	1	30
β-strand	347-355	9	31
β-strand	362-364	3	32
β-strand	372-376	5	32
β-strand	380-385	6	32
α-helix	387-398	12
α-helix	403-405	3
β-strand	413-419	7	32
α-helix	424	1
β-strand	425-431	7	33
β-strand	434-440	7	33
β-strand	445-449	5	33

Chain H: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	970-973	4	34
α-helix	976-981	6
β-strand	990	1	35
β-strand	994-997	4	34
β-strand	1001-1005	5	34
β-strand	1009	1	35
α-helix	1018-1021	4
β-strand	1024-1027	4	29
β-strand	1030-1033	4	29
α-helix	1041-1042	2
β-strand	1051-1055	5	34
β-strand	1061	1	36
β-strand	1068	1	36
α-helix	1075-1085	11
β-strand	1091-1095	5	34
β-strand	1102-1106	5	34

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1432-1454	23

Chain J: 16 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-13	3
β-strand	24-29	6	37
β-strand	34-39	6	37
β-strand	42-47	6	37
β-strand	55-58	4	37
β-strand	70-73	4	38
β-strand	79-83	5	38
β-strand	87-92	6	38
α-helix	103-107	5
β-strand	110-115	6	38
α-helix	116-118	3
α-helix	125-126	2
β-strand	127-132	6	39
β-strand	136	1	40
α-helix	137-139	3
β-strand	141-146	6	39
β-strand	151-155	5	39
β-strand	164-166	3	39
β-strand	172-174	3	41
β-strand	182-187	6	42
β-strand	194-198	5	42
β-strand	204-208	5	42
β-strand	215-217	3	40
α-helix	220-235	16
α-helix	243-262	20
β-strand	264	1	40
β-strand	269-271	3	40
α-helix	274-277	4
β-strand	282	1	42
α-helix	284-285	2
β-strand	286-288	3	43
α-helix	290-291	2
α-helix	293-296	4
β-strand	299-306	8	43
β-strand	313-319	7	43
β-strand	323-329	7	43
α-helix	332-333	2
β-strand	342	1	42
β-strand	347-355	9	43
β-strand	362-364	3	44
β-strand	372-376	5	44
β-strand	380-385	6	44
α-helix	387-399	13
α-helix	403-405	3
β-strand	413-419	7	44
α-helix	424	1
β-strand	425-431	7	45
β-strand	434-440	7	45
β-strand	445-449	5	45

Chain K: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	970-973	4	46
α-helix	976-981	6
β-strand	990	1	47
β-strand	994-997	4	46
β-strand	1001-1005	5	46
β-strand	1009	1	47
α-helix	1018-1021	4
β-strand	1024-1027	4	41
β-strand	1030-1033	4	41
β-strand	1051-1055	5	46
β-strand	1061	1	48
β-strand	1068	1	48
α-helix	1075-1085	11
β-strand	1091-1095	5	46
β-strand	1102-1106	5	46

1 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
Nucleoporin NUP82	A, D, G, J	protein	452	Saccharomyces cerevisiae	P40368 (AlphaFold model)
Nucleoporin NUP116/NSP116	B, E, H, K	protein	148	Saccharomyces cerevisiae	Q02630 (AlphaFold model)
Nucleoporin NUP159	C, F, I, L	protein	36	Saccharomyces cerevisiae	P40477 (AlphaFold model)

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

>3PBP_1 Nucleoporin NUP82 (chains A, D, G, J)
MSQSSRLSALPIFQASLSASQSPRYIFSSQNGTRIVFIQDNIIRWYNVLTDSLYHSLNFS
RHLVLDDTFHVISSTSGDLLCLFNDNEIFVMEVPWGYSNVEDVSIQDAFQIFHYSIDEEE
VGPKSSIKKVLFHPKSYRDSCIVVLKEDDTITMFDILNSQEKPIVLNKPNNSFGLDARVN
DITDLEFSKDGLTLYCLNTTEGGDIFAFYPFLPSVLLLNEKDLNLILNKSLVMYESLDST
TDVIVKRNVIKQLQFVSKLHENWNSRFGKVDIQKEYRLAKVQGPFTINPFPGELYDYTAT
NIATILIDNGQNEIVCVSFDDGSLILLFKDLEMSMSWDVDNYVYNNSLVLIERVKLQREI
KSLITLPEQLGKLYVISDNIIQQVNFMSWASTLSKSINESDLNPLAGLKFESKLEDIATI
ERIPNLAYINWNDQSNLALMSNKTLTFQNISS

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

>3PBP_2 Nucleoporin NUP116/NSP116 (chains B, E, H, K)
MNENYYISPSLDTLSSYSLLQLRKVPHLVVGHKSYGKIEFLEPVDLAGIPLTSLGGVIIT
FEPKTCIIYANLPNRPKRGEGINVRARITCFNCYPVDKSTRKPIKDPNHQLVKRHIERLK
KNPNSKFESYDADSGTYVFIVNHAAEQT

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

>3PBP_3 Nucleoporin NUP159 (chains C, F, I, L)
SSITKDMKGFKVVEVGLAMNTKKQIGDFFKNLNMAK

Primary citation

Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex. Yoshida, K., Seo, H.S., Debler, E.W. et al. Proc Natl Acad Sci U S A (2011) 108:16571-16576. DOI 10.1073/pnas.1112846108 · PubMed

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

3TKN 3.4 Å, Structure of the Nup82-Nup159-Nup98 heterotrimer
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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