6X08: Nup85-Seh1 from S. cerevisiae bound by VHH-SAN2

Nup85-Seh1 from S. cerevisiae bound by VHH-SAN2. Determined by X-ray diffraction at 4.19 Å resolution. Released 9 Dec 2020.

Method: X-ray diffraction
Resolution: 4.19 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Vicugna pacos
Chains: 3
Atoms: 6,827
Mol. weight: 117.61 kDa
Released: 9 Dec 2020

Explore 6X08 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X08 contains 32 α-helices and 40 β-strands across 3 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: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	12-17	6	2
β-strand	23-28	6	2
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	58-63	6	3
α-helix	64-65	2
α-helix	66-68	3
β-strand	71-76	6	3
β-strand	81-86	6	3
β-strand	98-104	7	3
β-strand	111-116	6	4
α-helix	117-118	2
α-helix	119-121	3
β-strand	124-129	6	4
β-strand	133-139	7	4
β-strand	148-155	8	4
β-strand	169-173	5	5
β-strand	182-187	6	5
β-strand	190-196	7	5
β-strand	202-207	6	5
β-strand	215-221	7	6
β-strand	229-235	7	6
β-strand	240-245	6	6
β-strand	294-300	7	6
β-strand	307-312	6	7
β-strand	319-323	5	7
β-strand	328-333	6	7
β-strand	339-345	7	7

Chain B: 27 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	48-49	2	7
β-strand	67-70	4	8
β-strand	79-82	4	8
β-strand	89-90	2	1
β-strand	91-92	2	8
α-helix	94-95	2
α-helix	102-118	17
α-helix	140-164	25
α-helix	170-189	20
α-helix	197-199	3
α-helix	201-215	15
α-helix	221-229	9
α-helix	243-253	11
α-helix	258-267	10
α-helix	270-276	7
α-helix	279-293	15
α-helix	300-318	19
α-helix	326-340	15
α-helix	343-348	6
α-helix	353-363	11
α-helix	368-370	3
α-helix	371-379	9
α-helix	391-398	8
α-helix	405-412	8
α-helix	414-426	13
α-helix	462-474	13
α-helix	482-490	9
α-helix	497-507	11
α-helix	508-510	3
α-helix	519-528	10
α-helix	532-542	11
α-helix	544-548	5

Chain K: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	9
β-strand	10-12	3	10
β-strand	18-23	6	9
β-strand	35-39	5	10
β-strand	45-50	6	10
β-strand	59-60	2	10
β-strand	68-72	5	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-97	6	10
β-strand	119-123	5	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoporin SEH1	A	protein	353	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53011 (AlphaFold model)
Nucleoporin NUP85	B	protein	568	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P46673 (AlphaFold model)
VHH-SAN2	K	protein	125	Vicugna pacos

Sequence of entity 1 (A), FASTA

>6X08_1 Nucleoporin SEH1 (chains A)
GPGSMQPFDSGHDDLVHDVVYDFYGRHVATCSSDQHIKVFKLDKDTSNWELSDSWRAHDS
SIVAIDWASPEYGRIIASASYDKTVKLWEEDPDQEECSGRRWNKLCTLNDSKGSLYSVKF
APAHLGLKLACLGNDGILRLYDALEPSDLRSWTLTSEMKVLSIPPANHLQSDFCLSWCPS
RFSPEKLAVSALEQAIIYQRGKDGKLHVAAKLPGHKSLIRSISWAPSIGRWYQLIATGCK
DGRIRIFKITEKLSPLASEESLTNSNMFDNSADVDMDAQGRSDSNTEEKAELQSNLQVEL
LSEHDDHNGEVWSVSWNLTGTILSSAGDDGKVRLWKATYSNEFKCMSVITAQQ

Sequence of entity 2 (B), FASTA

>6X08_2 Nucleoporin NUP85 (chains B)
MADPMTIDDSNRLLMDVDQFDFLDDGTAQLSNNKTDEEEQLYKRDPVSGAILVPMTVNDQ
PIEKNGDKMPLKFKLGPLSYQNMAFITAKDKYKLYPVRIPRLDTSKEFSAYVSGLFEIYR
DLGDDRVFNVPTIGVVNSNFAKEHNATVNLAMEAILNELEVFIGRVKDQDGRVNRFYELE
ESLTVLNCLRTMYFILDGQDVEENRSEFIESLLNWINRSDGEPDEEYIEQVFSVKDSTAG
KKVFETQYFWKLLNQLVLRGLLSQAIGCIERSDLLPYLSDTCAVSFDAVSDSIELLKQYP
KDSSSTFREWKNLVLKLSQAFGSSATDISGELRDYIEDFLLVIGGNQRKILQYSRTWYES
FCGFLLYYIPSLELSAEYLQMSLEANVVDITNDWEQPCVDIISGKIHSILPVMESLDSCT
AAFTAMICEAKGLIENIFEGEKNSDDYSNEDNEMLEDLFSYRNGMASYMLNSFAFELCSL
GDKELWPVAIGLIALSATGTRSAKKMVIAELLPHYPFVTNDDIEWMLSICVEWRLPEIAK
EIYTTLGNQMLSAHNIIESIANFSRAGK

Sequence of entity 3 (K), FASTA

>6X08_3 VHH-SAN2 (chains K)
QVQLVETGGGLVQPGGSLRLSCAASGFTLDDYAIGWFRQAPGKEREGVSCISRSGGSTTY
TDSVKGRFTISRDNAENTVYLQMNSLKPEDTAVYYCAAARTRGTCWLNRIGMDYWGKGTQ
VTVSS

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 P53011 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3F3F 2.9 Å, Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21
8ADL 2.95 Å, Cryo-EM structure of the SEA complex
3F3P 3.2 Å, Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21212
9H5K 3.2 Å, Cryo-EM structure of the SEAC-EGOC supercomplex
3EWE 3.5 Å, Crystal Structure of the Nup85/Seh1 Complex
3F3G 3.75 Å, Crystal structure of the nucleoporin pair Nup85-Seh1, space group P212121
4XMM 7.38 Å, Structure of the yeast coat nucleoporin complex, space group C2
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

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