6X06: Nucleoporin NUP120

Nup120 (aa1-757) from S. cerevisiae bound by VHH-SAN11. Determined by X-ray diffraction at 4.27 Å resolution. Released 9 Dec 2020.

Method: X-ray diffraction
Resolution: 4.27 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Vicugna pacos
Chains: 2
Atoms: 5,650
Mol. weight: 101.12 kDa
Released: 9 Dec 2020

Explore 6X06 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X06 contains 20 α-helices and 48 β-strands across 2 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: 19 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	4-10	7	2
β-strand	23-26	4	3
β-strand	57-61	5	3
β-strand	67-71	5	3
β-strand	80-83	4	3
β-strand	92-95	4	3
β-strand	101	1	4
β-strand	108-112	5	5
β-strand	116-122	7	5
β-strand	123	1	4
β-strand	128-134	7	5
α-helix	135-139	5
β-strand	151-153	3	5
β-strand	167-169	3	6
β-strand	173-177	5	6
β-strand	183-186	4	6
β-strand	205	1	6
β-strand	226-229	4	7
β-strand	233-236	4	7
β-strand	244	1	7
β-strand	256	1	7
β-strand	280-283	4	8
β-strand	286-291	6	8
β-strand	297-301	5	8
β-strand	321	1	8
β-strand	330-337	8	9
β-strand	349-357	9	9
β-strand	360-368	9	9
α-helix	370-372	3
β-strand	376-379	4	9
β-strand	380	1	1
β-strand	385	1	2
α-helix	386-392	7
α-helix	404-414	11
α-helix	417-429	13
β-strand	433	1	10
α-helix	441-457	17
β-strand	460-466	7	2
β-strand	470-475	6	2
β-strand	480-486	7	2
α-helix	487	1
α-helix	489-495	7
α-helix	506-517	12
α-helix	522-537	16
α-helix	546-553	8
α-helix	554-558	5
α-helix	564-574	11
α-helix	579-584	6
α-helix	585-591	7
α-helix	610-639	30
α-helix	648-669	22
α-helix	672-682	11
α-helix	695-710	16

Chain K: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	11-13	3	12
β-strand	18-24	7	11
β-strand	37-39	3	13
β-strand	45-46	2	13
β-strand	52	1	14
β-strand	57	1	14
β-strand	68-72	5	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	93-95	3	13
β-strand	103	1	10
β-strand	118-119	2	13
β-strand	121-123	3	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoporin NUP120	A	protein	758	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P35729 (AlphaFold model)
VHH-SAN11	K	protein	124	Vicugna pacos

Sequence of entity 1 (A), FASTA

>6X06_1 Nucleoporin NUP120 (chains A)
SMACLSRIDANLLQYYEKPEPNNTVDLYVSNNSNNNGLKEGDKSISTPVPQPYGSEYSNC
LLLSNSEYICYHFSSRSTLLTFYPLSDAYHGKTINIHLPNASMNQRYTLTIQEVEQQLLV
NVILKDGSFLTLQLPLSFLFSSANTLNGEWFHLQNPYDFTVRVPHFLFYVSPQFSVVFLE
DGGLLGLKKVDGVHYEPLLFNDNSYLKSLTRFFSRSSKSDYDSVISCKLFHERYLIVLTQ
NCHLKIWDLTSFTLIQDYDMVSQSDSDPSHFRKVEAVGEYLSLYNNTLVTLLPLENGLFQ
MGTLLVDSSGILTYTFQNNIPTNLSASAIWSIVDLVLTRPLELNVEASYLNLIVLWKSGT
ASKLQILNVNDESFKNYEWIESVNKSLVDLQSEHDLDIVTKTGDVERGFCNLKSRYGTQI
FERAQQILSENKIIMAHNEDEEYLANLETILRDVKTAFNEASSITLYGDEIILVNCFQPY
NHSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVLRSISKKFLDIITGE
LPDSMTTVEKFTDIFKNCLENQFEITNLKILFDELNSFDIPVVLNDLINNQMKPGIFWKK
DFISAIKFDGFTSIISLESLHQLLSIHYRITLQVLLTFVLFDLDTEIFGQHISTLLDLHY
KQFLLLNLYRQDKCLLAEVLLKDSSEFSFGVKFFNYGQLIAYIDSLNSNVYNASITENSF
FMTFFRSYIIENTSHKNIRFFLENVECPFYLRHNEVQE

Sequence of entity 2 (K), FASTA

>6X06_2 VHH-SAN11 (chains K)
QVQLVETGGGLVRAGGSLRLSCVDSGRTFRVYTMGWFRQAPGKEREFVAAIRWSGDRTYY
GDPVQGRFTISRDKGKNTVYLQMNSLKPEDTAVYYCAAPAGGGVVYDDHKAYAYWGQGTQ
VTVS

Primary citation

A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure. Nordeen, S.A., Andersen, K.R., Knockenhauer, K.E. et al. Nat Commun (2020) 11:6179-6179. DOI 10.1038/s41467-020-19884-6 · PubMed

Other PDB entries of the same protein (UniProt P35729 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3F7F 2.6 Å, Structure of Nup120
3H7N 3.0 Å, Structure of Nup120
3HXR 3.0 Å, Nucleoporin Nup120 from S.cerevisiae (aa 1-757)
4XMM 7.38 Å, Structure of the yeast coat nucleoporin complex, space group C2
4XMN 7.6 Å, Structure of the yeast coat nucleoporin complex, space group P212121
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

Browse structure collections

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