3F3F: Nucleoporin pair Nup85-Seh1, space group P21

Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21. Determined by X-ray diffraction at 2.9 Å resolution. Released 7 Apr 2009.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 25,239
Mol. weight: 417.34 kDa
Released: 7 Apr 2009

Explore 3F3F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3F3F contains 139 α-helices and 120 β-strands across 8 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: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
α-helix	11	1
β-strand	12-17	6	2
β-strand	23-28	6	2
β-strand	32-38	7	2
β-strand	45-52	8	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	133-138	6	4
β-strand	149-155	7	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	215-220	6	6
α-helix	221-222	2
β-strand	229-235	7	6
β-strand	240-247	8	6
β-strand	292-300	9	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: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
α-helix	11	1
β-strand	12-17	6	9
β-strand	23-28	6	9
β-strand	32-38	7	9
β-strand	45-52	8	9
β-strand	58-63	6	10
α-helix	64-65	2
β-strand	67	1	11
β-strand	69	1	11
β-strand	71-76	6	10
β-strand	81-86	6	10
β-strand	98-104	7	10
β-strand	111-116	6	12
α-helix	117-118	2
α-helix	119-121	3
β-strand	124-129	6	12
β-strand	133-138	6	12
β-strand	149-155	7	12
β-strand	169-173	5	13
β-strand	182-187	6	13
β-strand	190-196	7	13
β-strand	202-207	6	13
β-strand	215-220	6	14
α-helix	221-222	2
β-strand	229-235	7	14
β-strand	240-247	8	14
β-strand	292-300	9	14
β-strand	307-312	6	15
β-strand	319-323	5	15
β-strand	328-333	6	15
β-strand	339-345	7	15

Chain C: 29 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	48-49	2	7
β-strand	67-74	8	1
β-strand	77-82	6	1
β-strand	89-91	3	1
α-helix	102-117	16
α-helix	119-122	4
α-helix	135-164	30
α-helix	170-189	20
α-helix	197-200	4
α-helix	201-215	15
α-helix	221-227	7
α-helix	243-254	12
α-helix	258-265	8
α-helix	270-275	6
α-helix	276	1
α-helix	279-292	14
α-helix	300-318	19
α-helix	326-340	15
α-helix	343-348	6
α-helix	353-359	7
α-helix	360-364	5
α-helix	368-370	3
α-helix	371-381	11
α-helix	391-398	8
α-helix	403-405	3
α-helix	406-412	7
α-helix	414-427	14
α-helix	461-474	14
α-helix	482-491	10
α-helix	497-507	11
α-helix	508-510	3
α-helix	516-529	14
α-helix	532-543	12

Chain D: 30 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	48-49	2	15
β-strand	67-74	8	8
β-strand	77-82	6	8
β-strand	89-91	3	8
α-helix	102-117	16
α-helix	119-122	4
α-helix	136-165	30
α-helix	170-189	20
α-helix	197-200	4
α-helix	201-215	15
α-helix	221-228	8
α-helix	244-254	11
α-helix	258-265	8
α-helix	270-275	6
α-helix	276	1
α-helix	279-292	14
α-helix	300-318	19
α-helix	326-340	15
α-helix	343-348	6
α-helix	353-359	7
α-helix	360-364	5
α-helix	368-370	3
α-helix	371-381	11
α-helix	391-398	8
α-helix	403-405	3
α-helix	406-412	7
α-helix	414-427	14
α-helix	461-474	14
α-helix	482-491	10
α-helix	497-507	11
α-helix	508-510	3
α-helix	516-529	14
α-helix	532-542	11
α-helix	544-548	5

Chain E: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	1B	1	16
β-strand	4-5	2	17
α-helix	11	1
β-strand	12-17	6	18
β-strand	23-28	6	18
β-strand	32-38	7	18
β-strand	45-52	8	18
β-strand	58-63	6	19
α-helix	64-65	2
α-helix	66-68	3
β-strand	71-76	6	19
β-strand	81-86	6	19
β-strand	98-104	7	19
β-strand	111-116	6	20
α-helix	117-118	2
α-helix	119-121	3
β-strand	124-129	6	20
β-strand	133-139	7	20
β-strand	148-155	8	20
β-strand	169-173	5	21
β-strand	182-187	6	21
β-strand	190-196	7	21
β-strand	202-207	6	21
β-strand	215-220	6	22
α-helix	221-222	2
β-strand	229-235	7	22
β-strand	240-247	8	22
β-strand	292-300	9	22
β-strand	307-312	6	23
β-strand	319-323	5	23
β-strand	328-333	6	23
β-strand	339-345	7	23

Chain F: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	24
α-helix	11	1
β-strand	12-17	6	25
β-strand	23-28	6	25
β-strand	32-38	7	25
β-strand	45-52	8	25
β-strand	58-63	6	26
α-helix	64-65	2
β-strand	67	1	27
β-strand	69	1	27
β-strand	71-76	6	26
β-strand	81-86	6	26
β-strand	98-104	7	26
β-strand	111-116	6	28
α-helix	117-118	2
α-helix	119-121	3
β-strand	124-129	6	28
β-strand	133-139	7	28
β-strand	148-155	8	28
β-strand	169-173	5	29
β-strand	182-187	6	29
β-strand	190-196	7	29
β-strand	202-207	6	29
β-strand	215-220	6	30
α-helix	221-222	2
β-strand	229-235	7	30
β-strand	240-247	8	30
β-strand	292-300	9	30
β-strand	307-312	6	31
β-strand	319-323	5	31
β-strand	328-333	6	31
β-strand	339-345	7	31

Chain G: 29 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	67-74	8	17
β-strand	77-82	6	17
β-strand	89-91	3	17
β-strand	93	1	16
α-helix	102-117	16
α-helix	119-122	4
α-helix	135-166	32
α-helix	170-189	20
α-helix	197-200	4
α-helix	201-215	15
α-helix	221-227	7
α-helix	243-254	12
α-helix	258-265	8
α-helix	270-275	6
α-helix	276	1
α-helix	279-292	14
α-helix	300-318	19
α-helix	326-340	15
α-helix	343-348	6
α-helix	353-359	7
α-helix	360-364	5
α-helix	368-370	3
α-helix	371-381	11
α-helix	391-398	8
α-helix	403-405	3
α-helix	406-412	7
α-helix	414-427	14
α-helix	461-474	14
α-helix	482-491	10
α-helix	497-507	11
α-helix	508-510	3
α-helix	516-529	14
α-helix	532-545	14

Chain H: 29 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	67-74	8	24
β-strand	77-82	6	24
β-strand	89-93	5	24
α-helix	102-117	16
α-helix	119-122	4
α-helix	135-165	31
α-helix	170-189	20
α-helix	197-200	4
α-helix	201-215	15
α-helix	221-227	7
α-helix	243-254	12
α-helix	258-265	8
α-helix	270-275	6
α-helix	276	1
α-helix	279-292	14
α-helix	300-318	19
α-helix	326-340	15
α-helix	343-348	6
α-helix	353-359	7
α-helix	360-364	5
α-helix	368-370	3
α-helix	371-381	11
α-helix	391-398	8
α-helix	403-405	3
α-helix	406-412	7
α-helix	414-427	14
α-helix	461-474	14
α-helix	482-491	10
α-helix	497-507	11
α-helix	508-510	3
α-helix	516-529	14
α-helix	532-543	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoporin SEH1	A, B, E, F	protein	351	Saccharomyces cerevisiae	P53011 (AlphaFold model)
Nucleoporin NUP85	C, D, G, H	protein	570	Saccharomyces cerevisiae	P46673 (AlphaFold model)

Sequence of entity 1 (A, B, E, F), FASTA

>3F3F_1 Nucleoporin SEH1 (chains A, B, E, F)
PHMQPFDSGHDDLVHDVVYDFYGRHVATCSSDQHIKVFKLDKDTSNWELSDSWRAHDSSI
VAIDWASPEYGRIIASASYDKTVKLWEEDPDQEECSGRRWNKLCTLNDSKGSLYSVKFAP
AHLGLKLACLGNDGILRLYDALEPSDLRSWTLTSEMKVLSIPPANHLQSDFCLSWCPSRF
SPEKLAVSALEQAIIYQRGKDGKLHVAAKLPGHKSLIRSISWAPSIGRWYQLIATGCKDG
RIRIFKITEKLSPLASEESLTNSNMFDNSADVDMDAQGRSDSNTEEKAELQSNLQVELLS
EHDDHNGEVWSVSWNLTGTILSSAGDDGKVRLWKATYSNEFKCMSVITAQQ

Sequence of entity 2 (C, D, G, H), FASTA

>3F3F_2 Nucleoporin NUP85 (chains C, D, G, H)
MTIDDSNRLLMDVDQFDFLDDGTAQLSNNKTDEEEQLYKRDPVSGAILVPMTVNDQPIEK
NGDKMPLKFKLGPLSYQNMAFITAKDKYKLYPVRIPRLDTSKEFSAYVSGLFEIYRDLGD
DRVFNVPTIGVVNSNFAKEHNATVNLAMEAILNELEVFIGRVKDQDGRVNRFYELEESLT
VLNCLRTMYFILDGQDVEENRSEFIESLLNWINRSDGEPDEEYIEQVFSVKDSTAGKKVF
ETQYFWKLLNQLVLRGLLSQAIGCIERSDLLPYLSDTCAVSFDAVSDSIELLKQYPKDSS
STFREWKNLVLKLSQAFGSSATDISGELRDYIEDFLLVIGGNQRKILQYSRTWYESFCGF
LLYYIPSLELSAEYLQMSLEANVVDITNDWEQPCVDIISGKIHSILPVMESLDSCTAAFT
AMICEAKGLIENIFEGEKNSDDYSNEDNEMLEDLFSYRNGMASYMLNSFAFELCSLGDKE
LWPVAIGLIALSATGTRSAKKMVIAELLPHYPFVTNDDIEWMLSICVEWRLPEIAKEIYT
TLGNQMLSAHNIIESIANFSRAGKYELVKS

Primary citation

A fence-like coat for the nuclear pore membrane. Debler, E.W., Ma, Y., Seo, H.S. et al. Mol Cell (2008) 32:815-826. DOI 10.1016/j.molcel.2008.12.001 · PubMed

Other PDB entries of the same protein (UniProt P53011 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
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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