8BSH: COPII inner coat

COPII inner coat. Determined by electron microscopy at 3.8 Å resolution. Released 18 Jan 2023.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 13,635
Mol. weight: 211.22 kDa
Ligands: MG, GNP
Released: 18 Jan 2023

Explore 8BSH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BSH contains 85 α-helices and 94 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: 37 helices, 44 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
β-strand	12-14	3	1
β-strand	16	1	2
β-strand	18-19	2	3
α-helix	23-28	6
α-helix	32-33	2
β-strand	34-37	4	1
β-strand	48-49	2	3
α-helix	52-54	3
β-strand	55	1	4
β-strand	64	1	4
β-strand	70-72	3	5
β-strand	77-79	3	5
β-strand	86-87	2	5
α-helix	91-93	3
α-helix	98-100	3
α-helix	103-105	3
β-strand	109-112	4	3
α-helix	116	1
β-strand	117	1	3
α-helix	118	1
β-strand	123-129	7	6
α-helix	134-148	15
β-strand	156-162	7	6
β-strand	166-169	4	6
β-strand	177-182	6	6
α-helix	190-198	9
α-helix	208-217	10
α-helix	224-227	4
β-strand	229-230	2	6
α-helix	231-243	13
α-helix	252-253	2
β-strand	256	1	7
α-helix	262-276	15
β-strand	283-288	6	6
β-strand	303	1	7
α-helix	307-309	3
α-helix	311-316	6
α-helix	323-338	16
β-strand	342-348	7	6
α-helix	355-363	9
β-strand	371-372	2	6
α-helix	378-385	8
β-strand	399-408	10	3
β-strand	412	1	8
β-strand	414	1	9
β-strand	416-418	3	1
β-strand	422-423	2	3
β-strand	432	1	9
β-strand	439	1	1
β-strand	444-450	7	3
β-strand	456-459	4	1
β-strand	462	1	8
β-strand	484-495	12	3
β-strand	499-511	13	3
α-helix	517-520	4
β-strand	523	1	2
α-helix	525-539	15
α-helix	545-561	17
β-strand	565	1	10
α-helix	571-573	3
β-strand	575	1	10
α-helix	582-587	6
α-helix	603-615	13
α-helix	618-625	8
β-strand	628-632	5	11
β-strand	640	1	11
β-strand	644	1	12
α-helix	645-647	3
β-strand	653-657	5	11
β-strand	661-666	6	11
α-helix	668-675	8
α-helix	678-680	3
α-helix	685-701	17
α-helix	708-709	2
β-strand	710-715	6	11
α-helix	722-727	6
β-strand	729	1	12
α-helix	730	1
α-helix	750-751	2
α-helix	752-764	13

Chain B: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	24
α-helix	37-45	9
α-helix	52-54	3
β-strand	58-62	5	24
β-strand	69-73	5	24
α-helix	79-86	8
β-strand	93-96	4	24
β-strand	99	1	25
α-helix	103-105	3
α-helix	106-117	12
α-helix	120-122	3
β-strand	128-129	2	24
β-strand	132	1	25
α-helix	142-149	8
α-helix	164-165	2
β-strand	168	1	24
β-strand	172	1	26
β-strand	177	1	26
α-helix	180-186	7

Chain C: 39 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	135-138	4
β-strand	141-142	2	13
α-helix	152-155	4
α-helix	157-161	5
α-helix	177-178	2
β-strand	182-184	3	14
β-strand	186	1	15
β-strand	189-190	2	16
α-helix	193-199	7
β-strand	204-207	4	14
α-helix	219-221	3
β-strand	222-223	2	17
β-strand	230	1	18
α-helix	236	1
β-strand	237	1	18
α-helix	238	1
β-strand	243-245	3	19
β-strand	250-252	3	19
β-strand	259-261	3	19
α-helix	264-269	6
α-helix	276-278	3
α-helix	281-284	4
β-strand	287-291	5	17
α-helix	292-293	2
α-helix	301-303	3
β-strand	305-311	7	6
α-helix	314-318	5
α-helix	321-330	10
α-helix	333-335	3
β-strand	344-350	7	6
β-strand	354-358	5	6
α-helix	362-365	4
β-strand	374-378	5	6
β-strand	394-395	2	6
α-helix	397-399	3
α-helix	400-413	14
α-helix	424-434	11
β-strand	441-445	5	6
α-helix	471	1
α-helix	472-476	5
α-helix	481-492	12
β-strand	496-499	4	6
β-strand	502-503	2	20
α-helix	509-518	10
β-strand	526-527	2	20
α-helix	534-548	15
β-strand	553-562	10	17
β-strand	566-572	7	14
β-strand	576	1	17
β-strand	583-585	3	17
β-strand	594-600	7	14
β-strand	608-619	12	17
β-strand	623-634	12	17
β-strand	635-636	2	16
α-helix	639-645	7
β-strand	646	1	15
α-helix	650-665	16
α-helix	668-689	22
β-strand	702-703	2	13
α-helix	710-718	9
α-helix	730-739	10
α-helix	745-752	8
α-helix	754	1
β-strand	755-758	4	21
β-strand	769-771	3	22
α-helix	776	1
β-strand	777-781	5	22
α-helix	782-785	4
β-strand	800-803	4	21
β-strand	807-812	6	21
α-helix	818-824	7
β-strand	836	1	21
α-helix	847-860	14
β-strand	870-875	6	21
α-helix	888-899	12
β-strand	907	1	23
β-strand	910	1	23
α-helix	911-912	2
α-helix	913-924	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein transport protein SEC23	A	protein	768	Saccharomyces cerevisiae	P15303 (AlphaFold model)
SEC24 isoform 1	C	protein	926	Saccharomyces cerevisiae	P40482 (AlphaFold model)
Small COPII coat GTPase SAR1	B	protein	190	Saccharomyces cerevisiae	P20606 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8BSH_1 Protein transport protein SEC23 (chains A)
MDFETNEDINGVRFTWNVFPSTRSDANSNVVPVGCLYTPLKEYDELNVAPYNPVVCSGPH
CKSILNPYCVIDPRNSSWSCPICNSRNHLPPQYTNLSQENMPLELQSTTIEYITNKPVTV
PPIFFFVVDLTSETENLDSLKESIITSLSLLPPNALIGLITYGNVVQLHDLSSETIDRCN
VFRGDREYQLEALTEMLTGQKPTGPGGAASHLPNAMNKVTPFSLNRFFLPLEQVEFKLNQ
LLENLSPDQWSVPAGHRPLRATGSALNIASLLLQGCYKNIPARIILFASGPGTVAPGLIV
NSELKDPLRSHHDIDSDHAQHYKKACKFYNQIAQRVAANGHTVDIFAGCYDQIGMSEMKQ
LTDSTGGVLLLTDAFSTAIFKQSYLRLFAKDEEGYLKMAFNGNMAVKTSKDLKVQGLIGH
ASAVKKTDANNISESEIGIGATSTWKMASLSPYHSYAIFFEIANTAANSNPMMSAPGSAD
RPHLAYTQFITTYQHSSGTNRIRVTTVANQLLPFGTPAIAASFDQEAAAVLMARIAVHKA
ETDDGADVIRWLDRTLIKLCQKYADYNKDDPQSFRLAPNFSLYPQFTYYLRRSQFLSVFN
NSPDETAFYRHIFTREDTTNSLIMIQPTLTSFSMEDDPQPVLLDSISVKPNTILLLDTFF
FILIYHGEQIAQWRKAGYQDDPQYADFKALLEEPKLEAAELLVDRFPLPRFIDTEAGGSQ
ARFLLSKLNPSDNYQDMARGGSTIVLTDDVSLQNFMTHLQQVAVSGQA

Sequence of entity 2 (C), FASTA

>8BSH_2 SEC24 isoform 1 (chains C)
MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ
FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA
YGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPD
YIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPLNEDGLIVRCRRCRSYMNP
FVTFIEQGRRWRCNFCRLANDVPMQMDQSDPNDPKSRYDRNEIKCAVMEYMAPKEYTLRQ
PPPATYCFLIDVSQSSIKSGLLATTINTLLQNLDSIPNHDERTRISILCVDNAIHYFKIP
LDSENNEESADQINMMDIADLEEPFLPRPNSMVVSLKACRQNIETLLTKIPQIFQSNLIT
NFALGPALKSAYHLIGGVGGKIIVVSGTLPNLGIGKLQRRNESGVVNTSKETAQLLSCQD
SFYKNFTIDCSKVQITVDLFLASEDYMDVASLSNLSRFTAGQTHFYPGFSGKNPNDIVKF
STEFAKHISMDFCMETVMRARGSTGLRMSRFYGHFFNRSSDLCAFSTMPRDQSYLFEVNV
DESIMADYCYVQVAVLLSLNNSQRRIRIITLAMPTTESLAEVYASADQLAIASFYNSKAV
EKALNSSLDDARVLINKSVQDILATYKKEIVVSNTAGGAPLRLCANLRMFPLLMHSLTKH
MAFRSGIVPSDHRASALNNLESLPLKYLIKNIYPDVYSLHDMADEAGLPVQTEDGEATGT
IVLPQPINATSSLFERYGLYLIDNGNELFLWMGGDAVPALVFDVFGTQDIFDIPIGKQEI
PVVENSEFNQRVRNIINQLRNHDDVITYQSLYIVRGASLSEPVNHASAREVATLRLWASS
TLVEDKILNNESYREFLQIMKARISK

Sequence of entity 3 (B), FASTA

>8BSH_3 Small COPII coat GTPase SAR1 (chains B)
MAGWDIFGWFRDVLASLGLWNKHGKLLFLGLDNAGKTTLLHMLKNDRLATLQPTWHPTSE
ELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIA
ELKDVPFVILGNKIDAPNAVSEAELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYL
EAFQWLSQYI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1

Primary citation

A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0. Zivanov, J., Oton, J., Ke, Z. et al. Elife (2022) 11. DOI 10.7554/eLife.83724 · PubMed

Other PDB entries of the same protein (UniProt P15303 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1M2O 2.5 Å, Crystal Structure of the Sec23-Sar1 complex
2QTV 2.5 Å, Structure of Sec23-Sar1 complexed with the active fragment of Sec31
1M2V 2.75 Å, Crystal Structure of the yeast Sec23/24 heterodimer
6ZGA 4.6 Å, COPII on membranes, inner coat
6GNI 4.9 Å, Cryo-tomography and subtomogram averaging of Sar1-Sec23-Sec24 - fitted model.
4BZI 23.0 Å, The structure of the COPII coat assembled on membranes

Browse structure collections

About this viewer

MolViewer shows 8BSH directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.