3EWE: Nup85/Seh1 Complex

Crystal Structure of the Nup85/Seh1 Complex. Determined by X-ray diffraction at 3.5 Å resolution. Released 11 Nov 2008.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 9,689
Mol. weight: 206.76 kDa
Released: 11 Nov 2008

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

Secondary structure: helices and β-sheets

3EWE contains 45 α-helices and 59 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.

Chain A: 1 helix, 27 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
β-strand	23-27	5	1
β-strand	32-38	7	1
β-strand	45-52	8	1
β-strand	60-63	4	2
β-strand	71-75	5	2
β-strand	81-85	5	2
β-strand	99-104	6	2
β-strand	113-116	4	3
α-helix	117-118	2
β-strand	124	1	4
β-strand	125-128	4	3
β-strand	135	1	3
β-strand	137-138	2	4
β-strand	150-151	2	4
β-strand	170-173	4	5
β-strand	183-186	4	5
β-strand	191-195	5	5
β-strand	203-207	5	5
β-strand	215-220	6	6
β-strand	229-235	7	6
β-strand	240-245	6	6
β-strand	292	1	6
β-strand	295-297	3	6
β-strand	307-311	5	7
β-strand	319-323	5	7
β-strand	327-333	7	7
β-strand	339-346	8	7

Chain B: 22 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	70	1	8
β-strand	78-81	4	8
β-strand	90-93	4	8
α-helix	104-117	14
α-helix	139-163	25
α-helix	170-189	20
α-helix	201-213	13
α-helix	220-224	5
α-helix	243-254	12
α-helix	258-265	8
α-helix	279-289	11
α-helix	304-316	13
α-helix	327-340	14
α-helix	343-346	4
α-helix	353-363	11
α-helix	371-381	11
α-helix	391-399	9
α-helix	403-405	3
α-helix	406-427	22
α-helix	462-473	12
α-helix	482-489	8
α-helix	497-507	11
α-helix	508-510	3
α-helix	516-529	14
α-helix	532-553	22

Chain C: 1 helix, 27 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	9
β-strand	23-27	5	9
β-strand	32-38	7	9
β-strand	45-52	8	9
β-strand	60-63	4	10
β-strand	72-75	4	10
β-strand	81-85	5	10
β-strand	99-104	6	10
β-strand	113-116	4	11
α-helix	117-118	2
β-strand	124	1	12
β-strand	125-128	4	11
β-strand	135	1	11
β-strand	137-138	2	12
β-strand	150-151	2	12
β-strand	170-173	4	13
β-strand	183-186	4	13
β-strand	191-194	4	13
β-strand	204-207	4	13
β-strand	215-220	6	14
β-strand	229-235	7	14
β-strand	240-245	6	14
β-strand	294	1	14
β-strand	297	1	14
β-strand	307-311	5	15
β-strand	319-323	5	15
β-strand	327-333	7	15
β-strand	339-346	8	15

Chain D: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	78-81	4	16
β-strand	90-93	4	16
α-helix	104-117	14
α-helix	139-163	25
α-helix	170-189	20
α-helix	201-213	13
α-helix	220-224	5
α-helix	243-254	12
α-helix	258-265	8
α-helix	279-289	11
α-helix	304-316	13
α-helix	328-340	13
α-helix	353-363	11
α-helix	371-381	11
α-helix	391-399	9
α-helix	403-405	3
α-helix	406-427	22
α-helix	462-473	12
α-helix	482-489	8
α-helix	497-507	11
α-helix	508-510	3
α-helix	516-529	14
α-helix	532-554	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoporin SEH1	A, C	protein	349	Saccharomyces cerevisiae	P53011 (AlphaFold model)
Nucleoporin NUP85	B, D	protein	564	Saccharomyces cerevisiae	P46673 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3EWE_1 Nucleoporin SEH1 (chains A, C)
MQPFDSGHDDLVHDVVYDFYGRHVATCSSDQHIKVFKLDKDTSNWELSDSWRAHDSSIVA
IDWASPEYGRIIASASYDKTVKLWEEDPDQEECSGRRWNKLCTLNDSKGSLYSVKFAPAH
LGLKLACLGNDGILRLYDALEPSDLRSWTLTSEMKVLSIPPANHLQSDFCLSWCPSRFSP
EKLAVSALEQAIIYQRGKDGKLHVAAKLPGHKSLIRSISWAPSIGRWYQLIATGCKDGRI
RIFKITEKLSPLASEESLTNSNMFDNSADVDMDAQGRSDSNTEEKAELQSNLQVELLSEH
DDHNGEVWSVSWNLTGTILSSAGDDGKVRLWKATYSNEFKCMSVITAQQ

Sequence of entity 2 (B, D), FASTA

>3EWE_2 Nucleoporin NUP85 (chains B, D)
MTIDDSNRLLMDVDQFDFLDDGTAQLSNNKTDEEEQLYKRDPVSGAILVPMTVNDQPIEK
NGDKMPLKFKLGPLSYQNMAFITAKDKYKLYPVRIPRLDTSKEFSAYVSGLFEIYRDLGD
DRVFNVPTIGVVNSNFAKEHNATVNLAMEAILNELEVFIGRVKDQDGRVNRFYELEESLT
VLNCLRTMYFILDGQDVEENRSEFIESLLNWINRSDGEPDEEYIEQVFSVKDSTAGKKVF
ETQYFWKLLNQLVLRGLLSQAIGCIERSDLLPYLSDTCAVSFDAVSDSIELLKQYPKDSS
STFREWKNLVLKLSQAFGSSATDISGELRDYIEDFLLVIGGNQRKILQYSRTWYESFCGF
LLYYIPSLELSAEYLQMSLEANVVDITNDWEQPCVDIISGKIHSILPVMESLDSCTAAFT
AMICEAKGLIENIFEGEKNSDDYSNEDNEMLEDLFSYRNGMASYMLNSFAFELCSLGDKE
LWPVAIGLIALSATGTRSAKKMVIAELLPHYPFVTNDDIEWMLSICVEWRLPEIAKEIYT
TLGNQMLSAHNIIESIANFSRAGK

Primary citation

Structural evidence for common ancestry of the nuclear pore complex and vesicle coats. Brohawn, S.G., Leksa, N.C., Spear, E.D. et al. Science (2008) 322:1369-1373. DOI 10.1126/science.1165886 · 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
3F3G 3.75 Å, Crystal structure of the nucleoporin pair Nup85-Seh1, space group P212121
6X08 4.19 Å, Nup85-Seh1 from S. cerevisiae bound by VHH-SAN2
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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