4XMN: Protein transport protein SEC13

Name: PDB 4XMN: Structure of the yeast coat nucleoporin complex, space group P212121
Published: 2015-03-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: protein transport

Structure of the yeast coat nucleoporin complex, space group P212121. Determined by X-ray diffraction at 7.6 Å resolution. Released 25 Mar 2015.

Method: X-ray diffraction
Resolution: 7.6 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae, synthetic construct
Chains: 7
Atoms: 19,816
Mol. weight: 413.53 kDa
Released: 25 Mar 2015

Explore 4XMN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XMN contains 134 α-helices and 113 β-strands across 7 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	12-17	6	1
β-strand	23-28	6	1
β-strand	32-37	6	1
β-strand	44-50	7	1
β-strand	56-58	3	2
β-strand	61	1	2
α-helix	64-66	3
β-strand	69-74	6	2
β-strand	79-84	6	2
β-strand	89-95	7	2
β-strand	102-105	4	3
α-helix	107-109	3
α-helix	110-112	3
β-strand	116-120	5	3
β-strand	124-130	7	3
β-strand	136-142	7	3
β-strand	148-153	6	4
β-strand	172-177	6	4
β-strand	181-186	6	4
α-helix	194	1
β-strand	195-201	7	4
β-strand	209-212	4	5
β-strand	220-225	6	5
β-strand	231-236	6	5
β-strand	247	1	5
β-strand	257-262	6	6
β-strand	269-273	5	6
β-strand	278-283	6	6
β-strand	289-291	3	6

Chain B: 34 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	152-154	3	7
β-strand	160-163	4	7
β-strand	171-174	4	7
α-helix	176-178	3
α-helix	183-186	4
α-helix	188-195	8
β-strand	198-202	5	8
β-strand	209-214	6	8
α-helix	218-221	4
α-helix	222-224	3
α-helix	230-242	13
α-helix	244-245	2
α-helix	254-287	34
α-helix	291-300	10
α-helix	304-313	10
α-helix	317-323	7
β-strand	326	1	9
β-strand	328	1	9
α-helix	331-344	14
α-helix	353-362	10
α-helix	373-378	6
α-helix	382-391	10
α-helix	400-408	9
α-helix	412-414	3
α-helix	418-428	11
α-helix	429-431	3
α-helix	432-442	11
α-helix	448-460	13
α-helix	468-484	17
α-helix	488-495	8
α-helix	501-515	15
α-helix	523-529	7
α-helix	535-549	15
α-helix	555-559	5
α-helix	567-575	9
α-helix	588-601	14
α-helix	613-623	11
α-helix	632-644	13
α-helix	655-672	18
α-helix	682-686	5
α-helix	704-711	8

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	554-559	6
α-helix	568-584	17
α-helix	591-596	6
α-helix	606-609	4
α-helix	617-633	17
α-helix	639-654	16
α-helix	662-674	13
α-helix	686-698	13
α-helix	708-718	11
α-helix	726-743	18

Chain E: 40 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	12
β-strand	23-27	5	13
β-strand	56-61	6	13
α-helix	66	1
β-strand	67-72	6	13
β-strand	78-83	6	13
α-helix	84-86	3
β-strand	92-96	5	13
β-strand	101	1	14
α-helix	104-107	4
β-strand	108-112	5	15
β-strand	116-122	7	15
β-strand	123	1	14
β-strand	128-134	7	15
α-helix	135-139	5
β-strand	150-151	2	15
β-strand	163-168	6	16
β-strand	173-178	6	16
β-strand	183-188	6	16
β-strand	194-196	3	16
α-helix	198-200	3
α-helix	203-208	6
β-strand	223-229	7	17
β-strand	233-238	6	17
β-strand	242-247	6	17
β-strand	252-258	7	17
α-helix	259-261	3
β-strand	280-282	3	18
β-strand	286-291	6	18
β-strand	297-304	8	18
β-strand	312-320	9	18
β-strand	330-337	8	19
β-strand	349-357	9	19
β-strand	360-368	9	19
β-strand	376-380	5	19
β-strand	381-385	5	12
α-helix	386-393	8
α-helix	404-415	12
α-helix	417-429	13
α-helix	440-457	18
β-strand	460-466	7	12
β-strand	470-475	6	12
β-strand	480-486	7	12
α-helix	489-495	7
α-helix	505-517	13
α-helix	522-537	16
α-helix	546-553	8
α-helix	554-558	5
α-helix	564-575	12
α-helix	579-585	7
α-helix	586-591	6
α-helix	594-596	3
β-strand	603	1	20
α-helix	609-639	31
α-helix	648-670	23
α-helix	672-680	9
β-strand	690	1	20
α-helix	695-710	16
α-helix	716-725	10
α-helix	736-739	4
α-helix	755-765	11
α-helix	771-780	10
α-helix	808-816	9
α-helix	822-831	10
α-helix	839-852	14
α-helix	863-878	16
α-helix	885-894	10
α-helix	902-912	11
α-helix	918-930	13
α-helix	944-954	11
α-helix	961-970	10
α-helix	977-986	10
α-helix	995-1007	13
α-helix	1026-1035	10

Chain F: 30 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	12-24	13
α-helix	36-54	19
α-helix	61-86	26
α-helix	92-94	3
α-helix	102-112	11
α-helix	114-128	15
α-helix	133-136	4
α-helix	145-150	6
α-helix	160-163	4
α-helix	166-168	3
α-helix	171-189	19
α-helix	193-202	10
α-helix	206-213	8
β-strand	217	1	10
α-helix	218	1
β-strand	219	1	11
α-helix	225-227	3
β-strand	235	1	11
β-strand	237	1	10
α-helix	240-252	13
α-helix	258-267	10
α-helix	274-277	4
α-helix	282-304	23
α-helix	310-312	3
α-helix	321-323	3
α-helix	324-334	11
α-helix	336-340	5
α-helix	342-351	10
α-helix	355-364	10
α-helix	383-399	17
α-helix	406-422	17
α-helix	426-428	3
α-helix	429-433	5
α-helix	437-441	5

Chain H: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	26
β-strand	36-38	3	27
β-strand	44-51	8	26
α-helix	55-57	3
β-strand	59-65	7	27
β-strand	71-78	8	27
β-strand	84-86	3	27
β-strand	94-99	6	26
α-helix	100-102	3
β-strand	104-109	6	26
α-helix	114-116	3
β-strand	118-124	7	27
β-strand	139-140	2	27
β-strand	144-148	5	27
β-strand	154	1	28
α-helix	155-156	2
β-strand	157-161	5	29
α-helix	162-164	3
β-strand	172-182	11	29
β-strand	183	1	28
β-strand	188-191	4	30
α-helix	192-194	3
β-strand	200-202	3	29
α-helix	203-205	3
β-strand	206-207	2	29
β-strand	213-222	10	29
α-helix	223-225	3
β-strand	231-237	7	30
α-helix	238-240	3
β-strand	242-248	7	30
α-helix	250-252	3

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	21
β-strand	13-15	3	22
β-strand	22-28	7	21
β-strand	37-41	5	22
β-strand	48-52	5	22
β-strand	56-57	2	22
α-helix	58	1
β-strand	65-70	6	21
β-strand	73-78	6	21
β-strand	87-92	6	22
β-strand	101	1	22
β-strand	102	1	21
β-strand	105-108	4	22
β-strand	114	1	23
α-helix	115-116	2
β-strand	117-121	5	24
α-helix	122-124	3
α-helix	125-128	4
β-strand	132-142	11	24
β-strand	143	1	23
β-strand	148-153	6	25
β-strand	156-157	2	25
β-strand	162-166	5	24
α-helix	167-170	4
β-strand	176-185	10	24
α-helix	186-190	5
β-strand	194-200	7	25
β-strand	208-213	6	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein transport protein SEC13	A	protein	297	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q04491 (AlphaFold model)
Nucleoporin NUP145	B	protein	652	Saccharomyces cerevisiae	P49687 (AlphaFold model)
Nucleoporin NUP84	F	protein	454	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P52891 (AlphaFold model)
Nucleoporin NUP120	E	protein	1045	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P35729 (AlphaFold model)
Nucleoporin NUP85	D	protein	685	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P46673
Antibody 87 light chain	L	protein	217	synthetic construct
Antibody 87 heavy chain	H	protein	267	synthetic construct

Sequence of entity 1 (A), FASTA

>4XMN_1 Protein transport protein SEC13 (chains A)
MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVD
WAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVAS
SDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADN
LVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQ
GPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

Sequence of entity 2 (B), FASTA

>4XMN_2 Nucleoporin NUP145 (chains B)
MGSSHHHHHHSDQPDADFEGIEASPKLDVSKDWVEQLILAGSSLRSVFATSKEFDGPCQN
EIDLLFSECNDEIDNAKLIMKERRFTASYTFAKFSTGSMLLTKDIVGKSGVSIKRLPTEL
QRKFLFDDVYLDKEIEKVTIEARKSNPYPQISESSLLFKDALDYMEKTSSDYNLWKLSSI
LFDPVSYPYKTDNDQVKMALLKKERHCRLTSWIVSQIGPEIEEKIRNSSNEIEQIFLYLL
LNDVVRASKLAIESKNGHLSVLISYLGSNDPRIRDLAELQLQKWSTGGCSIDKNISKIYK
LLSGSPFEGLFSLKELESEFSWLCLLNLTLCYGQIDEYSLESLVQSHLDKFSLPYDDPIG
VIFQLYAANENTEKLYKEVRQRTNALDVQFCWYLIQTLRFNGTRVFSKETSDEATFAFAA
QLEFAQLHGHSLFVSCFLNDDKAAEDTIKRLVMREITLLRASTNDHILNRLKIPSQLIFN
AQALKDRYEGNYLSEVQNLLLGSSYDLAEMAIVTSLGPRLLLSNNPVQNNELKTLREILN
EFPDSERDKWSVSINVFEVYLKLVLDNVETQETIDSLISGMKIFYDQYKHCREVAACCNV
MSQEIVSKILEKNNPSIGDSKAKLLELPLGQPEKAYLRGEFAQDLMKCTYKI

Sequence of entity 3 (F), FASTA

>4XMN_3 Nucleoporin NUP84 (chains F)
GPHMELSPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSG
DESNVISSKDWELEARFWHLVELLLVFRNADLDLDEMELHPYNSRGLFEKKLMQDNKQLY
QIWIVMVWLKENTYVMERPKNVPTSKWLNSITSGGLKSCDLDFPLRENTNVLDVKDKEED
HIFFKYIYELILAGAIDEALEEAKLSDNISICMILCGIQEYLNPVIDTQIANEFNTQQGI
KKHSLWRRTVYSLSQQAGLDPYERAIYSYLSGAIPNQEVLQYSDWESDLHIHLNQILQTE
IENYLLENNQVGTDELILPLPSHALTVQEVLNRVASRHPSESEHPIRVLMASVILDSLPS
VIHSSVEMLLDVVKGTEASNDIIDKPYLLRIVTHLAICLDIINPGSVEEVDKSKLITTYI
SLLKLQGLYENIPIYATFLNESDCLEACSFILSS

Sequence of entity 4 (E), FASTA

>4XMN_4 Nucleoporin NUP120 (chains E)
MHHHHHHSMACLSRIDANLLQYYEKPEPNNTVDLYVSNNSNNNGLKEGDKSISTPVPQPY
GSEYSNCLLLSNSEYICYHFSSRSTLLTFYPLSDAYHGKTINIHLPNASMNQRYTLTIQE
VEQQLLVNVILKDGSFLTLQLPLSFLFSSANTLNGEWFHLQNPYDFTVRVPHFLFYVSPQ
FSVVFLEDGGLLGLKKVDGVHYEPLLFNDNSYLKSLTRFFSRSSKSDYDSVISCKLFHER
YLIVLTQNCHLKIWDLTSFTLIQDYDMVSQSDSDPSHFRKVEAVGEYLSLYNNTLVTLLP
LENGLFQMGTLLVDSSGILTYTFQNNIPTNLSASAIWSIVDLVLTRPLELNVEASYLNLI
VLWKSGTASKLQILNVNDESFKNYEWIESVNKSLVDLQSEHDLDIVTKTGDVERGFCNLK
SRYGTQIFERAQQILSENKIIMAHNEDEEYLANLETILRDVKTAFNEASSITLYGDEIIL
VNCFQPYNHSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVLRSISKKF
LDIITGELPDSMTTVEKFTDIFKNCLENQFEITNLKILFDELNSFDIPVVLNDLINNQMK
PGIFWKKDFISAIKFDGFTSIISLESLHQLLSIHYRITLQVLLTFVLFDLDTEIFGQHIS
TLLDLHYKQFLLLNLYRQDKCLLAEVLLKDSSEFSFGVKFFNYGQLIAYIDSLNSNVYNA
SITENSFFMTFFRSYIIENTSHKNIRFFLENVECPFYLRHNEVQEFMFAMTLFSCGNFDQ
SYEIFQLHDYPEAINDKLPTFLEDLKSENYHGDSIWKDLLCTFTVPYRHSAFYYQLSLLF
DRNNSQEFALKCISKSAEYSLKEIQIEELQDFKEKQHIHYLNLLIHFRMFEEVLDVLRLG
HECLSDTVRTNFLQLLLQEDIYSRDFFSTLLRLCNAHSDNGELYLRTVDIKIVDSILSQN
LRSGDWECFKKLYCFRMLNKSERAAAEVLYQYILMQADLDVIRKRKCYLMVINVLSSFDS
AYDQWILNGSKVVTLTDLRDELRGL

Sequence of entity 5 (D), FASTA

>4XMN_5 Nucleoporin NUP85 (chains D)
MGSSHHHHHHSDQPLSYQNMAFITAKDKYKLYPVRIPRLDTSKEFSAYVSGLFEIYRDLG
DDRVFNVPTIGVVNSNFAKEHNATVNLAMEAILNELEVFIGRVKDQDGRVNRFYELEESL
TVLNCLRTMYFILDGQDVEENRSEFIESLLNWINRSDGEPDEEYIEQVFSVKDSTAGKKV
FETQYFWKLLNQLVLRGLLSQAIGCIERSDLLPYLSDTCAVSFDAVSDSIELLKQYPKDS
SSTFREWKNLVLKLSQAFGSSATDISGELRDYIEDFLLVIGGNQRKILQYSRTWYESFCG
FLLYYIPSLELSAEYLQMSLEANVVDITNDWEQPCVDIISGKIHSILPVMESLDSCTAAF
TAMICEAKGLIENIFEGEKNSDDYSNEDNEMLEDLFSYRNGMASYMLNSFAFELCSLGDK
ELWPVAIGLIALSATGTRSAKKMVIAELLPHYPFVTNDDIEWMLSICVEWRLPEIAKEIY
TTLGNQMLSAHNIIESIANFSRAGKYELVKSYSWLLFEASCMEGQKLDDPVLNAIVSKNS
PAEDDVIIPQDILDCVVTNSMRQTLAPYAVLSQFYELRDREDWGQALRLLLLLIEFPYLP
KHYLVLLVAKFLYPIFLLDDKKLMDEDSVATVIEVIETKWDDADEKSSNLYETIIEADKS
LPSSMATLLKNLRKKLNFKLCQAFM

Sequence of entity 6 (L), FASTA

>4XMN_6 Antibody 87 light chain (chains L)
MASDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSG
VPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFI
FPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 7 (H), FASTA

>4XMN_7 Antibody 87 heavy chain (chains H)
MKKNIAFLLASMFVFSIATNAYAEISEVQLVESGGGLVQPGGSLRLSCAASGFNFSSSSI
HWVRQAPGKGLEWVASISSYYGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVY
YCARYETLYWPYQNSGMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVK
DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPS
NTKVDKKVEPKSCDKTHTGGSHHHHHH

Primary citation

Nuclear pores. Architecture of the nuclear pore complex coat. Stuwe, T., Correia, A.R., Lin, D.H. et al. Science (2015) 347:1148-1152. DOI 10.1126/science.aaa4136 · PubMed

Other PDB entries of the same protein (UniProt Q04491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PM7 2.35 Å, Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat,…
2PM6 2.45 Å, Crystal Structure of yeast Sec13/31 edge element of the COPII vesicular coat, native…
3JRP 2.6 Å, SEC13 with NUP145C (AA109-179) insertion blade
3MZK 2.69 Å, Sec13/Sec16 complex, S.cerevisiae
3MZL 2.8 Å, Sec13/Sec31 edge element, loop deletion mutant
8ADL 2.95 Å, Cryo-EM structure of the SEA complex
3IKO 3.2 Å, Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex
9H5K 3.2 Å, Cryo-EM structure of the SEAC-EGOC supercomplex
2PM9 3.3 Å, Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat
3JRO 4.0 Å, NUP84-NUP145C-SEC13 edge element of the NPC lattice
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

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