3F7F: Nup120

Structure of Nup120. Determined by X-ray diffraction at 2.6 Å resolution. Released 18 Aug 2009.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 22,876
Mol. weight: 337.93 kDa
Ligands: HG
Released: 18 Aug 2009

Explore 3F7F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3F7F contains 96 α-helices and 148 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.

Chains A, B and C: 24 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	1
β-strand	23-26	4	2
β-strand	56-61	6	2
β-strand	67-72	6	2
β-strand	78-83	6	2
α-helix	84-86	3
α-helix	91	1
β-strand	92-96	5	2
β-strand	101	1	3
α-helix	104-107	4
β-strand	108-112	5	4
β-strand	116-122	7	4
β-strand	123	1	3
β-strand	128-134	7	4
α-helix	135-139	5
β-strand	150	1	4
β-strand	163-168	6	5
β-strand	173	1	6
β-strand	174-178	5	5
β-strand	183-184	2	5
β-strand	187-188	2	6
β-strand	194-195	2	6
α-helix	198-200	3
α-helix	203-208	6
β-strand	223-229	7	7
β-strand	233-238	6	7
β-strand	242-247	6	7
β-strand	252-258	7	7
β-strand	280-282	3	8
β-strand	286-291	6	8
β-strand	297-304	8	8
β-strand	312-314	3	8
β-strand	318-320	3	8
β-strand	330-337	8	9
β-strand	349-357	9	9
β-strand	360-368	9	9
β-strand	376-379	4	9
β-strand	380-381	2	1
α-helix	386-392	7
α-helix	406-415	10
α-helix	417-428	12
α-helix	440-457	18
β-strand	460-466	7	1
β-strand	470-475	6	1
β-strand	480-486	7	1
α-helix	487	1
α-helix	489-494	6
α-helix	505-517	13
α-helix	522-537	16
α-helix	546-553	8
α-helix	554-558	5
α-helix	564-574	11
α-helix	579-585	7
α-helix	586-591	6
β-strand	603	1	10
α-helix	609-639	31
α-helix	648-670	23
α-helix	672-680	9
β-strand	690	1	10
α-helix	695-711	17
α-helix	719-728	10

Chain D: 24 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	31
β-strand	23-26	4	32
β-strand	56-61	6	32
β-strand	67-72	6	32
β-strand	78-83	6	32
α-helix	84-86	3
α-helix	91	1
β-strand	92-96	5	32
β-strand	101	1	33
α-helix	104-107	4
β-strand	108-112	5	34
β-strand	116-122	7	34
β-strand	123	1	33
β-strand	128-134	7	34
α-helix	135-139	5
β-strand	150	1	34
β-strand	163-168	6	35
β-strand	173	1	36
β-strand	174-178	5	35
β-strand	183-184	2	35
β-strand	187-188	2	36
β-strand	194-195	2	36
α-helix	198-200	3
α-helix	203-208	6
β-strand	223-229	7	37
β-strand	233-238	6	37
β-strand	242-247	6	37
β-strand	252-258	7	37
β-strand	280-282	3	38
β-strand	286-291	6	38
β-strand	297-304	8	38
β-strand	312-314	3	38
β-strand	318-320	3	38
β-strand	330-337	8	39
β-strand	349-357	9	39
β-strand	360-368	9	39
β-strand	376-379	4	39
β-strand	380-381	2	31
α-helix	386-392	7
α-helix	406-415	10
α-helix	417-429	13
α-helix	440-457	18
β-strand	460-466	7	31
β-strand	470-475	6	31
β-strand	480-486	7	31
α-helix	487	1
α-helix	489-494	6
α-helix	505-517	13
α-helix	522-537	16
α-helix	546-553	8
α-helix	554-558	5
α-helix	564-574	11
α-helix	579-585	7
α-helix	586-591	6
β-strand	603	1	40
α-helix	609-639	31
α-helix	648-670	23
α-helix	672-680	9
β-strand	690	1	40
α-helix	695-711	17
α-helix	719-728	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoporin NUP120	A, B, C, D	protein	729	Saccharomyces cerevisiae	P35729 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3F7F_1 Nucleoporin NUP120 (chains A, B, C, D)
MACLSRIDANLLQYYEKPEPNNTVDLYVSNNSNNNGLKEGDKSISTPVPQPYGSEYSNCL
LLSNSEYICYHFSSRSTLLTFYPLSDAYHGKTINIHLPNASMNQRYTLTIQEVEQQLLVN
VILKDGSFLTLQLPLSFLFSSANTLNGEWFHLQNPYDFTVRVPHFLFYVSPQFSVVFLED
GGLLGLKKVDGVHYEPLLFNDNSYLKCLTRFFSRSSKSDYDSVISCKLFHERYLIVLTQN
CHLKIWDLTSFTLIQDYDMVSQSDSDPSHFRKVEAVGEYLSLYNNTLVTLLPLENGLFQM
GTLLVDSSGILTYTFQNNIPTNLSASAIWSIVDLVLTRPLELNVEASYLNLIVLWKSGTA
SKLQILNVNDESFKNYEWIESVNKSLVDLQSEHDLDIVTKTGDVERGFCNLKSRYGTQIF
ERAQQILSENKIIMAHNEDEEYLANLETILRDVKTAFNEASSITLYGDEIILVNCFQPYN
HSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVLRSISKKFLDIITGEL
PDSMTTVEKFTDIFKNCLENQFEITNLKILFDELNSFDIPVVLNDLINNQMKPGIFWKKD
FISAIKFDGFTSIISLESLHQLLSIHYRITLQVLLTFVLFDLDTEIFGQHISTLLDLHYK
QFLLLNLYRQDKCLLAEVLLKDSSEFSFGVKFFNYGQLIAYIDSLNSNVYNASITENSFF
MTFFRSYII

Ligands and cofactors

ID	Name	Formula	Copies
HG	Mercury (II) ion	Hg	12

Primary citation

Structural and functional analysis of Nup120 suggests ring formation of the Nup84 complex. Seo, H.S., Ma, Y., Debler, E.W. et al. Proc Natl Acad Sci U S A (2009) 106:14281-14286. DOI 10.1073/pnas.0907453106 · PubMed

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

3H7N 3.0 Å, Structure of Nup120
3HXR 3.0 Å, Nucleoporin Nup120 from S.cerevisiae (aa 1-757)
6X06 4.27 Å, Nup120 (aa1-757) from S. cerevisiae bound by VHH-SAN11
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

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