6X04: Nucleoporin NUP133

Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN5. Determined by X-ray diffraction at 2.68 Å resolution. Released 9 Dec 2020.

Method: X-ray diffraction
Resolution: 2.68 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Vicugna pacos
Chains: 12
Atoms: 20,015
Mol. weight: 367.49 kDa
Released: 9 Dec 2020

Explore 6X04 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X04 contains 32 α-helices and 244 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.

Chain A: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	63	1	1
β-strand	67-70	4	1
β-strand	87-91	5	2
β-strand	96-100	5	2
β-strand	104-109	6	2
β-strand	120-123	4	2
β-strand	137-140	4	3
β-strand	164-168	5	3
β-strand	171-175	5	3
α-helix	178-180	3
β-strand	193-197	5	3
β-strand	208-213	6	4
β-strand	219-223	5	4
β-strand	228-234	7	4
β-strand	240-247	8	4
β-strand	267-277	11	5
β-strand	280-287	8	5
β-strand	291-298	8	5
β-strand	305-311	7	5
α-helix	313-321	9
α-helix	325-327	3
β-strand	332-338	7	6
β-strand	344-353	10	6
β-strand	358-369	12	6
β-strand	374-382	9	6
β-strand	398-400	3	7
α-helix	402-405	4
β-strand	413-420	8	7
β-strand	423-430	8	7
α-helix	441-443	3
β-strand	444-448	5	7
β-strand	457-460	4	1
β-strand	464-468	5	1
β-strand	474-479	6	1

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	8
β-strand	10-12	3	6
β-strand	18-22	5	8
β-strand	33-39	7	6
β-strand	46-52	7	6
β-strand	55-58	4	6
α-helix	60-62	3
β-strand	66-70	5	8
β-strand	77-81	5	8
α-helix	86-88	3
β-strand	90-100	11	6
β-strand	103-108	6	6
β-strand	112-116	5	6

Chain C: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	63	1	9
β-strand	67-72	6	9
β-strand	87-91	5	10
β-strand	96-100	5	10
β-strand	105-109	5	10
β-strand	120-122	3	10
β-strand	137-140	4	11
β-strand	164-168	5	11
β-strand	171-175	5	11
β-strand	197	1	11
β-strand	208-214	7	12
β-strand	218-223	6	12
β-strand	228-231	4	12
β-strand	244-247	4	12
β-strand	267-272	6	13
β-strand	280-287	8	13
β-strand	291-298	8	13
β-strand	305-311	7	13
α-helix	313-321	9
α-helix	325-327	3
β-strand	332-338	7	7
β-strand	344-353	10	7
β-strand	358-369	12	7
β-strand	374-382	9	7
β-strand	398-400	3	14
β-strand	413-419	7	14
β-strand	423-430	8	14
α-helix	441-443	3
β-strand	444-448	5	14
α-helix	449-450	2
β-strand	455-460	6	9
β-strand	464-469	6	9
β-strand	474-479	6	9

Chains D and L: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	15
β-strand	10-12	3	7
β-strand	18-22	5	15
β-strand	33-39	7	7
β-strand	46-52	7	7
β-strand	55-58	4	7
β-strand	66-70	5	15
β-strand	77-81	5	15
α-helix	86-88	3
β-strand	90-100	11	7
β-strand	103-108	6	7
β-strand	112-116	5	7

Chain E: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	63	1	16
β-strand	67-70	4	16
β-strand	87-91	5	17
β-strand	96-100	5	17
β-strand	105-109	5	17
β-strand	120-121	2	17
β-strand	137-140	4	18
β-strand	164-168	5	18
β-strand	171-175	5	18
β-strand	193-197	5	18
β-strand	208-213	6	19
β-strand	219-223	5	19
β-strand	228-234	7	19
β-strand	240-247	8	19
β-strand	267-272	6	20
β-strand	280-287	8	20
β-strand	291-298	8	20
β-strand	305-311	7	20
α-helix	313-321	9
α-helix	325-327	3
β-strand	332-338	7	14
β-strand	344-353	10	14
β-strand	358-369	12	14
β-strand	374-382	9	14
β-strand	398-400	3	6
β-strand	417-420	4	6
β-strand	423-427	5	6
β-strand	444-448	5	6
α-helix	449-450	2
β-strand	455-460	6	16
β-strand	464-469	6	16
β-strand	474-479	6	16

Chain F: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	10-12	3	14
β-strand	18-25	8	21
β-strand	33-39	7	14
β-strand	45-52	8	14
β-strand	55-58	4	14
β-strand	66-70	5	21
β-strand	76-81	6	21
α-helix	86-88	3
β-strand	90-100	11	14
β-strand	103-108	6	14
β-strand	112-116	5	14

Chain G: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	60-63	4	22
β-strand	67-70	4	22
β-strand	87-91	5	23
β-strand	96-100	5	23
β-strand	104-109	6	23
β-strand	120-123	4	23
β-strand	137-140	4	24
β-strand	164-168	5	24
β-strand	171-175	5	24
α-helix	178-180	3
β-strand	193-197	5	24
β-strand	208-214	7	25
β-strand	218-223	6	25
β-strand	228-234	7	25
β-strand	240-247	8	25
β-strand	267-277	11	26
β-strand	280-287	8	26
β-strand	291-297	7	26
β-strand	305-311	7	26
α-helix	313-320	8
α-helix	325-327	3
β-strand	332-338	7	27
β-strand	344-353	10	27
β-strand	358-369	12	27
β-strand	374-382	9	27
β-strand	398-400	3	28
β-strand	416-420	5	28
β-strand	423-427	5	28
β-strand	444-448	5	28
α-helix	449-450	2
β-strand	455-460	6	22
β-strand	464-469	6	22
β-strand	474-479	6	22

Chain H: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	29
β-strand	10-12	3	27
β-strand	18-25	8	29
β-strand	33-39	7	27
β-strand	46-52	7	27
β-strand	55-58	4	27
α-helix	60-62	3
β-strand	63	1	29
β-strand	66-70	5	29
β-strand	76-81	6	29
α-helix	86-88	3
β-strand	90-100	11	27
β-strand	103-108	6	27
β-strand	112-116	5	27

3 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 NUP133	A, C, E, G, I, K	protein	428	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P36161 (AlphaFold model)
VHH-SAN5	B, D, F, H, J, L	protein	118	Vicugna pacos

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

>6X04_1 Nucleoporin NUP133 (chains A, C, E, G, I, K)
GFDNSKVFTENNRYIVKTLQTDYSSGFSNDDELNGYIDMQIGYGLVNDHKKVYIWNIHST
QKDTPYITVPFRSDDNDEIAVAPRCILTFPATMDESPLALNPNDQDETGGLIIIKGSKAI
YYEDINSINNLNFKLSEKFSHELELPINSSGGEKCDLMLNCEPAGIVLSTNMGRIFFITI
RNSMGKPQLKLGKLLNKPFKLGIWSKIFNTNSSVVSLRNGPILGKGTRLVYITTNKGIFQ
TWQLSATNSHPTKLIDVNIYEAILESLQDLYPFAHGTLKIWDSHPLQDESSQLFLSSIYD
SSCNETYYILSTIIFDSSSNSFTIFSTYRLNTFMESITDTKFKPKIFIPQMENANDTNEV
TSILVMFPNAVVITQVNSKLDSSYSMRRKWEDIVSLRNDIDIIGSGYDSKSLYVLTKQMG
VLQFFVKE

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

>6X04_2 VHH-SAN5 (chains B, D, F, H, J, L)
QVQLVESGGGLVQAGGSLRLSCAASGSIGSLDAMAWYRRAPGKQRERVASISRYGTYYVD
SVKGRFTISRDNAKNTVYLQMNSLKPEDTGVYYCKGVMEVGGVIDEYWGQGTQVTVSS

Primary citation

Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif. Nordeen, S.A., Turman, D.L., Schwartz, T.U. Nat Commun (2020) 11:6060-6060. DOI 10.1038/s41467-020-19885-5 · PubMed

Other PDB entries of the same protein (UniProt P36161 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KFO 1.9 Å, Crystal structure of the C-terminal domain from the nuclear pore complex component…
6X05 2.1 Å, Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN4
6X02 6.38 Å, Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8
6X03 7.3 Å, Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9
8TIE 8.1 Å, Double nuclear outer ring of Nup84-complexes from the yeast NPC
7N84 11.6 Å, Double nuclear outer ring from the isolated yeast NPC
7N9F 37.0 Å, Structure of the in situ yeast NPC
8ZZ1 Structure of the Nup84 sub-complex of the Nuclear Pore Complex
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
8ZZG Integrative structure-function mapping of the nucleoporin Nup133

Browse structure collections

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