6ZGA: COPII on membranes, inner coat

COPII on membranes, inner coat. Determined by electron microscopy at 4.6 Å resolution. Released 17 Feb 2021.

Method: Electron microscopy
Resolution: 4.6 Å
Organisms: Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 8
Atoms: 26,963
Mol. weight: 422.94 kDa
Ligands: ZN, GNP, MG
Released: 17 Feb 2021

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

Secondary structure: helices and β-sheets

6ZGA contains 148 α-helices and 184 β-strands across 6 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: 33 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	14	1	1
β-strand	19-20	2	2
α-helix	23-27	5
β-strand	34-37	4	1
β-strand	48	1	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	87-88	2	5
α-helix	103-105	3
β-strand	110-117	8	3
α-helix	121-122	2
β-strand	123-129	7	6
α-helix	134-150	17
β-strand	156-162	7	6
β-strand	166-169	4	6
β-strand	179-180	2	7
β-strand	181-182	2	6
α-helix	190-195	6
α-helix	205-207	3
α-helix	208-217	10
α-helix	225-227	3
β-strand	229-230	2	6
α-helix	231-243	13
β-strand	256	1	8
α-helix	257-259	3
α-helix	262-276	15
β-strand	283-288	6	6
β-strand	303	1	8
α-helix	311-315	5
α-helix	323-339	17
β-strand	342-347	6	6
β-strand	348	1	9
α-helix	355-357	3
α-helix	360-363	4
β-strand	369	1	6
β-strand	372	1	9
α-helix	378-384	7
β-strand	390	1	10
β-strand	396	1	10
β-strand	399-408	10	3
β-strand	412-418	7	1
β-strand	422-423	2	3
β-strand	439	1	1
β-strand	444-450	7	3
β-strand	456-462	7	1
β-strand	485-495	11	3
β-strand	499-509	11	3
β-strand	511-512	2	2
α-helix	517-521	5
α-helix	525-540	16
α-helix	545-563	19
β-strand	565-567	3	11
β-strand	570-575	6	11
α-helix	578-580	3
α-helix	582-591	10
α-helix	603-613	11
α-helix	618-625	8
α-helix	627	1
β-strand	628-632	5	12
α-helix	641-643	3
β-strand	653-657	5	12
β-strand	662-665	4	12
α-helix	668-675	8
α-helix	685-700	16
α-helix	708-711	4
β-strand	712-714	3	12
α-helix	719-721	3
α-helix	722-727	6
α-helix	749-751	3
α-helix	752-761	10

Chain B: 32 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	140-142	3	13
α-helix	151-155	5
α-helix	157-162	6
α-helix	177-178	2
β-strand	186	1	14
β-strand	189	1	15
β-strand	192	1	16
α-helix	193-199	7
β-strand	222-223	2	17
β-strand	244-245	2	18
β-strand	250-251	2	18
α-helix	274-276	3
α-helix	281-284	4
β-strand	288-291	4	17
α-helix	292	1
α-helix	300-302	3
β-strand	306-311	6	7
α-helix	314-319	6
α-helix	321-330	10
β-strand	344-345	2	19
β-strand	347-350	4	7
β-strand	354-355	2	7
β-strand	358	1	20
β-strand	374	1	20
β-strand	376-378	3	7
β-strand	394-395	2	19
α-helix	397-399	3
α-helix	400-413	14
α-helix	424-435	12
β-strand	440-446	7	7
α-helix	459-463	5
α-helix	482-493	12
β-strand	495-501	7	7
α-helix	510-517	8
β-strand	523-525	3	7
α-helix	535-548	14
β-strand	553-562	10	17
β-strand	566-572	7	21
β-strand	576	1	17
β-strand	582-585	4	17
β-strand	595-600	6	21
β-strand	603	1	16
β-strand	608-619	12	17
β-strand	623-634	12	17
β-strand	635	1	15
α-helix	639-644	6
β-strand	646	1	14
α-helix	648-665	18
α-helix	669-689	21
β-strand	702-704	3	13
α-helix	705-707	3
α-helix	710-718	9
α-helix	730-742	13
α-helix	745-752	8
β-strand	756	1	22
β-strand	757-758	2	23
α-helix	784-786	3
β-strand	787	1	22
α-helix	791-793	3
β-strand	799-803	5	23
β-strand	808-812	5	23
α-helix	818-824	7
α-helix	830-832	3
β-strand	836	1	24
α-helix	848-860	13
β-strand	873	1	24
β-strand	874-875	2	23
α-helix	885-898	14
α-helix	899-901	3
β-strand	907	1	25
β-strand	910	1	25
α-helix	913-923	11

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	24-30	7	26
α-helix	36-45	10
α-helix	52-54	3
β-strand	60-64	5	26
β-strand	67-73	7	26
α-helix	79-83	5
α-helix	84-87	4
β-strand	93-99	7	26
α-helix	106-117	12
α-helix	120-124	5
β-strand	127-132	6	26
α-helix	142-148	7
β-strand	168-169	2	26
β-strand	172	1	27
β-strand	177	1	27
α-helix	180-186	7

Chain E: 33 helices, 41 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	14	1	28
β-strand	16	1	29
β-strand	19-20	2	30
α-helix	23-28	6
α-helix	32-33	2
β-strand	35-37	3	28
β-strand	70-72	3	31
β-strand	77-79	3	31
β-strand	87-88	2	31
α-helix	89-90	2
α-helix	92-94	3
α-helix	103-105	3
β-strand	110-117	8	32
β-strand	123-128	6	33
β-strand	129	1	34
α-helix	134-150	17
β-strand	156-159	4	33
β-strand	160-162	3	34
β-strand	166-168	3	34
β-strand	180-182	3	34
α-helix	190-198	9
α-helix	205-207	3
α-helix	208-217	10
α-helix	224-226	3
β-strand	229-230	2	33
α-helix	235-243	9
α-helix	252-253	2
β-strand	256	1	35
α-helix	257-259	3
α-helix	262-276	15
β-strand	282-288	7	33
β-strand	303	1	35
α-helix	311-316	6
α-helix	323-339	17
β-strand	341-347	7	33
α-helix	355-357	3
α-helix	360-363	4
α-helix	367-369	3
α-helix	378-385	8
β-strand	390	1	36
β-strand	396	1	36
β-strand	399-408	10	32
β-strand	412-418	7	28
β-strand	422-423	2	32
β-strand	432	1	28
β-strand	439-440	2	28
β-strand	444-450	7	32
β-strand	456-462	7	28
β-strand	485-495	11	32
β-strand	499-509	11	32
β-strand	511-512	2	30
β-strand	523	1	29
α-helix	525-540	16
α-helix	546-563	18
β-strand	565	1	37
β-strand	575	1	37
α-helix	582-591	10
α-helix	603-613	11
α-helix	618-625	8
β-strand	628-632	5	38
β-strand	639-640	2	38
β-strand	644	1	39
α-helix	645-647	3
β-strand	653-657	5	38
β-strand	661-666	6	38
α-helix	668-676	9
α-helix	685-702	18
α-helix	708-709	2
β-strand	710-715	6	38
α-helix	722-727	6
β-strand	729	1	39
α-helix	750-751	2
α-helix	752-761	10

Chain F: 35 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	140-142	3	40
α-helix	143-145	3
α-helix	151-154	4
α-helix	157-162	6
β-strand	168	1	41
α-helix	177-178	2
β-strand	182	1	42
β-strand	186	1	43
β-strand	189-190	2	44
β-strand	192	1	45
α-helix	193-199	7
β-strand	206-207	2	42
α-helix	219-221	3
β-strand	222	1	46
β-strand	241	1	41
β-strand	245	1	47
β-strand	250	1	47
β-strand	261	1	47
α-helix	275-278	4
α-helix	281-284	4
β-strand	287-290	4	46
α-helix	300-302	3
β-strand	305	1	48
β-strand	307-311	5	34
α-helix	314-319	6
α-helix	321-330	10
β-strand	344-345	2	48
β-strand	347-350	4	34
β-strand	354-358	5	34
α-helix	359-361	3
β-strand	374-378	5	34
β-strand	394-395	2	48
α-helix	397-399	3
α-helix	400-413	14
α-helix	424-435	12
β-strand	440-445	6	34
β-strand	446	1	49
α-helix	471-474	4
α-helix	482-493	12
β-strand	495-498	4	34
β-strand	499-503	5	49
α-helix	509-517	9
β-strand	523-527	5	49
α-helix	534-549	16
β-strand	553	1	46
β-strand	556	1	50
β-strand	557-562	6	46
β-strand	566-568	3	51
β-strand	576	1	52
β-strand	584	1	52
β-strand	585	1	50
β-strand	594-595	2	42
β-strand	598-600	3	51
β-strand	603	1	45
β-strand	608-619	12	46
β-strand	623-634	12	46
β-strand	635-636	2	44
α-helix	639-644	6
β-strand	646	1	43
α-helix	648-665	18
α-helix	669-689	21
β-strand	702-704	3	40
α-helix	705-707	3
α-helix	710-717	8
α-helix	730-742	13
α-helix	745-752	8
β-strand	755-758	4	53
α-helix	759-761	3
α-helix	780-786	7
β-strand	787	1	53
α-helix	791-793	3
β-strand	800-803	4	53
β-strand	808-811	4	53
α-helix	818-824	7
α-helix	840-842	3
α-helix	847-860	14
β-strand	872-874	3	53
α-helix	875-878	4
α-helix	885-901	17
β-strand	907	1	54
β-strand	910	1	54
α-helix	913-924	12

Chain G: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	55
α-helix	36-45	10
α-helix	52-54	3
β-strand	58-64	7	55
β-strand	67-73	7	55
α-helix	79-86	8
β-strand	93-99	7	55
α-helix	106-118	13
α-helix	120-122	3
β-strand	127-132	6	55
α-helix	142-149	8
β-strand	166-170	5	55
β-strand	172	1	56
β-strand	177	1	56
α-helix	180-186	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein transport protein SEC23	A, E	protein	767	Saccharomyces cerevisiae	P15303 (AlphaFold model)
Protein transport protein SEC24	B, F	protein	926	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40482 (AlphaFold model)
Small COPII coat GTPase SAR1	C	protein	190	Saccharomyces cerevisiae	P20606 (AlphaFold model)
Pro-pro-pro	D, H	protein	3	Saccharomyces cerevisiae
Small COPII coat GTPase SAR1	G	protein	189	Saccharomyces cerevisiae	P20606 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>6ZGA_1 Protein transport protein SEC23 (chains A, E)
DFETNEDINGVRFTWNVFPSTRSDANSNVVPVGCLYTPLKEYDELNVAPYNPVVCSGPHC
KSILNPYCVIDPRNSSWSCPICNSRNHLPPQYTNLSQENMPLELQSTTIEYITNKPVTVP
PIFFFVVDLTSETENLDSLKESIITSLSLLPPNALIGLITYGNVVQLHDLSSETIDRCNV
FRGDREYQLEALTEMLTGQKPTGPGGAASHLPNAMNKVTPFSLNRFFLPLEQVEFKLNQL
LENLSPDQWSVPAGHRPLRATGSALNIASLLLQGCYKNIPARIILFASGPGTVAPGLIVN
SELKDPLRSHHDIDSDHAQHYKKACKFYNQIAQRVAANGHTVDIFAGCYDQIGMSEMKQL
TDSTGGVLLLTDAFSTAIFKQSYLRLFAKDEEGYLKMAFNGNMAVKTSKDLKVQGLIGHA
SAVKKTDANNISESEIGIGATSTWKMASLSPYHSYAIFFEIANTAANSNPMMSAPGSADR
PHLAYTQFITTYQHSSGTNRIRVTTVANQLLPFGTPAIAASFDQEAAAVLMARIAVHKAE
TDDGADVIRWLDRTLIKLCQKYADYNKDDPQSFRLAPNFSLYPQFTYYLRRSQFLSVFNN
SPDETAFYRHIFTREDTTNSLIMIQPTLTSFSMEDDPQPVLLDSISVKPNTILLLDTFFF
ILIYHGEQIAQWRKAGYQDDPQYADFKALLEEPKLEAAELLVDRFPLPRFIDTEAGGSQA
RFLLSKLNPSDNYQDMARGGSTIVLTDDVSLQNFMTHLQQVAVSGQA

Sequence of entity 2 (B, F), FASTA

>6ZGA_2 Protein transport protein SEC24 (chains B, F)
MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ
FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA
YGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPD
YIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPLNEDGLIVRCRRCRSYMNP
FVTFIEQGRRWRCNFCRLANDVPMQMDQSDPNDPKSRYDRNEIKCAVMEYMAPKEYTLRQ
PPPATYCFLIDVSQSSIKSGLLATTINTLLQNLDSIPNHDERTRISILCVDNAIHYFKIP
LDSENNEESADQINMMDIADLEEPFLPRPNSMVVSLKACRQNIETLLTKIPQIFQSNLIT
NFALGPALKSAYHLIGGVGGKIIVVSGTLPNLGIGKLQRRNESGVVNTSKETAQLLSCQD
SFYKNFTIDCSKVQITVDLFLASEDYMDVASLSNLSRFTAGQTHFYPGFSGKNPNDIVKF
STEFAKHISMDFCMETVMRARGSTGLRMSRFYGHFFNRSSDLCAFSTMPRDQSYLFEVNV
DESIMADYCYVQVAVLLSLNNSQRRIRIITLAMPTTESLAEVYASADQLAIASFYNSKAV
EKALNSSLDDARVLINKSVQDILATYKKEIVVSNTAGGAPLRLCANLRMFPLLMHSLTKH
MAFRSGIVPSDHRASALNNLESLPLKYLIKNIYPDVYSLHDMADEAGLPVQTEDGEATGT
IVLPQPINATSSLFERYGLYLIDNGNELFLWMGGDAVPALVFDVFGTQDIFDIPIGKQEI
PVVENSEFNQRVRNIINQLRNHDDVITYQSLYIVRGASLSEPVNHASAREVATLRLWASS
TLVEDKILNNESYREFLQIMKARISK

Sequence of entity 3 (C), FASTA

>6ZGA_3 Small COPII coat GTPase SAR1 (chains C)
MAGWDIFGWFRDVLASLGLWNKHGKLLFLGLDNAGKTTLLHMLKNDRLATLQPTWHPTSE
ELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIA
ELKDVPFVILGNKIDAPNAVSEAELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYL
EAFQWLSQYI

Sequence of entity 4 (D, H), FASTA

>6ZGA_4 PRO-PRO-PRO (chains D, H)
PPP

Sequence of entity 5 (G), FASTA

>6ZGA_5 Small COPII coat GTPase SAR1 (chains G)
MAGWDIFGWFRDVLASLGLWNKHGKLLFLGLDNAGKTTLLHMLKNDRLATLQPTWHPTSE
ELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIA
ELKDVPFVILGNKIDAPNAVSEAELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYL
EAFQWLSQY

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Structure of the complete, membrane-assembled COPII coat reveals a complex interaction network. Hutchings, J., Stancheva, V.G., Brown, N.R. et al. Nat Commun (2021) 12:2034-2034. DOI 10.1038/s41467-021-22110-6 · 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
8BSH 3.8 Å, COPII 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

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