6GNI: Protein transport protein SEC23

Name: PDB 6GNI: Cryo-tomography and subtomogram averaging of Sar1-Sec23-Sec24 - fitted model.
Published: 2018-10-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: protein transport

Cryo-tomography and subtomogram averaging of Sar1-Sec23-Sec24 - fitted model. Determined by electron microscopy at 4.9 Å resolution. Released 17 Oct 2018.

Method: Electron microscopy
Resolution: 4.9 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 3
Atoms: 12,937
Mol. weight: 194.1 kDa
Ligands: MG, GNP, ZN
Released: 17 Oct 2018

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

Secondary structure: helices and β-sheets

6GNI contains 79 α-helices and 89 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: 32 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	12-14	3	1
β-strand	16	1	2
β-strand	18-20	3	3
α-helix	23-28	6
α-helix	32	1
β-strand	33-37	5	1
β-strand	48-49	2	3
β-strand	55	1	4
β-strand	64	1	4
α-helix	69-70	2
β-strand	71-72	2	5
β-strand	77-79	3	5
β-strand	86-88	3	5
α-helix	89-90	2
α-helix	103-106	4
β-strand	109-117	9	3
α-helix	118	1
β-strand	123-129	7	6
α-helix	134-148	15
β-strand	156-162	7	6
β-strand	165-170	6	6
β-strand	178-183	6	6
α-helix	190-198	9
α-helix	224-227	4
β-strand	229-230	2	6
α-helix	231-244	14
β-strand	256	1	7
α-helix	262-276	15
β-strand	282-288	7	6
β-strand	303	1	7
α-helix	307-309	3
α-helix	311-315	5
α-helix	322-339	18
β-strand	341-348	8	6
α-helix	355-358	4
α-helix	360-363	4
β-strand	369-372	4	6
α-helix	378-386	9
β-strand	390	1	8
β-strand	396	1	8
β-strand	399-408	10	3
β-strand	412-418	7	1
β-strand	422-423	2	3
β-strand	432	1	1
β-strand	439	1	1
β-strand	444-450	7	3
β-strand	456-462	7	1
β-strand	484-495	12	3
β-strand	499-512	14	3
α-helix	517-521	5
β-strand	523	1	2
α-helix	525-540	16
α-helix	545-563	19
β-strand	565-567	3	9
β-strand	570-575	6	9
α-helix	583-591	9
α-helix	603-613	11
α-helix	618-625	8
β-strand	628-632	5	10
β-strand	639-640	2	10
β-strand	644	1	11
β-strand	653-657	5	10
β-strand	661-666	6	10
α-helix	668-676	9
α-helix	678-680	3
α-helix	686-702	17
α-helix	708-709	2
β-strand	710-715	6	10
α-helix	719-721	3
α-helix	722-725	4
β-strand	729	1	11
α-helix	749-751	3
α-helix	752-763	12

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	22
α-helix	36-45	10
α-helix	52-54	3
β-strand	58-62	5	22
β-strand	69-73	5	22
α-helix	78-87	10
β-strand	93-99	7	22
α-helix	103-105	3
α-helix	106-117	12
β-strand	127-132	6	22
α-helix	142-149	8
α-helix	164-165	2
β-strand	166-171	6	22
β-strand	172	1	23
β-strand	177	1	23
α-helix	179-186	8

Chain E: 39 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	135-138	4
β-strand	140-142	3	12
α-helix	153-155	3
α-helix	157-160	4
α-helix	165-167	3
β-strand	182-184	3	13
β-strand	186	1	14
β-strand	189-190	2	15
β-strand	192	1	16
α-helix	193-199	7
β-strand	204-207	4	13
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	262-263	2
α-helix	264-266	3
α-helix	274-279	6
α-helix	281-284	4
β-strand	287-291	5	17
α-helix	294-296	3
α-helix	302-304	3
β-strand	305	1	20
β-strand	306-311	6	6
α-helix	314-318	5
α-helix	321-331	11
β-strand	344-345	2	20
β-strand	347-350	4	6
β-strand	354-358	5	6
β-strand	374-378	5	6
β-strand	394-395	2	20
α-helix	400-413	14
α-helix	424-435	12
β-strand	440-446	7	6
α-helix	471	1
α-helix	472-476	5
α-helix	482-493	12
β-strand	495-503	9	6
α-helix	509-517	9
β-strand	523-527	5	6
α-helix	534-549	16
β-strand	553-562	10	17
β-strand	566-572	7	13
β-strand	576	1	17
β-strand	582-588	7	17
β-strand	594-600	7	13
β-strand	603	1	16
β-strand	608-619	12	17
β-strand	623-634	12	17
β-strand	635-636	2	15
α-helix	639-644	6
β-strand	646	1	14
α-helix	648-665	18
α-helix	669-685	17
α-helix	686-690	5
β-strand	702-704	3	12
α-helix	705-707	3
α-helix	710-718	9
α-helix	730-742	13
α-helix	745-752	8
β-strand	755-758	4	21
α-helix	780-782	3
α-helix	784-786	3
β-strand	787	1	21
β-strand	799-803	5	21
β-strand	807-812	6	21
α-helix	819-821	3
α-helix	849-858	10
α-helix	869	1
β-strand	870-874	5	21
α-helix	890-900	11
α-helix	910-912	3
α-helix	913-924	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein transport protein SEC23	A	protein	767	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P15303 (AlphaFold model)
Protein transport protein SEC24	E	protein	794	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40482 (AlphaFold model)
Small COPII coat GTPase SAR1	B	protein	167	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P20606 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6GNI_1 Protein transport protein SEC23 (chains A)
DFETNEDINGVRFTWNVFPSTRSDANSNVVPVGCLYTPLKEYDELNVAPYNPVVCSGPHC
KSILNPYCVIDPRNSSWSCPICNSRNHLPPQYTNLSQENMPLELQSTTIEYITNKPVTVP
PIFFFVVDLTSETENLDSLKESIITSLSLLPPNALIGLITYGNVVQLHDLSSETIDRCNV
FRGDREYQLEALTEMLTGQKPTGPGGAASHLPNAMNKVTPFSLNRFFLPLEQVEFKLNQL
LENLSPDQWSVPAGHRPLRATGSALNIASLLLQGCYKNIPARIILFASGPGTVAPGLIVN
SELKDPLRSHHDIDSDHAQHYKKACKFYNQIAQRVAANGHTVDIFAGCYDQIGMSEMKQL
TDSTGGVLLLTDAFSTAIFKQSYLRLFAKDEEGYLKMAFNGNMAVKTSKDLKVQGLIGHA
SAVKKTDANNISESEIGIGATSTWKMASLSPYHSYAIFFEIANTAANSNPMMSAPGSADR
PHLAYTQFITTYQHSSGTNRIRVTTVANQLLPFGTPAIAASFDQEAAAVLMARIAVHKAE
TDDGADVIRWLDRTLIKLCQKYADYNKDDPQSFRLAPNFSLYPQFTYYLRRSQFLSVFNN
SPDETAFYRHIFTREDTTNSLIMIQPTLTSFSMEDDPQPVLLDSISVKPNTILLLDTFFF
ILIYHGEQIAQWRKAGYQDDPQYADFKALLEEPKLEAAELLVDRFPLPRFIDTEAGGSQA
RFLLSKLNPSDNYQDMARGGSTIVLTDDVSLQNFMTHLQQVAVSGQA

Sequence of entity 2 (E), FASTA

>6GNI_2 Protein transport protein SEC24 (chains E)
RPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPDYIRSTLNAVPKN
SSLLKKSKLPFGLVIRPYQHLYDDIDPPPLNEDGLIVRCRRCRSYMNPFVTFIEQGRRWR
CNFCRLANDVPMQMDQSDPNDPKSRYDRNEIKCAVMEYMAPKEYTLRQPPPATYCFLIDV
SQSSIKSGLLATTINTLLQNLDSIPNHDERTRISILCVDNAIHYFKIPLDSENNEESADQ
INMMDIADLEEPFLPRPNSMVVSLKACRQNIETLLTKIPQIFQSNLITNFALGPALKSAY
HLIGGVGGKIIVVSGTLPNLGIGKLQRRNESGVVNTSKETAQLLSCQDSFYKNFTIDCSK
VQITVDLFLASEDYMDVASLSNLSRFTAGQTHFYPGFSGKNPNDIVKFSTEFAKHISMDF
CMETVMRARGSTGLRMSRFYGHFFNRSSDLCAFSTMPRDQSYLFEVNVDESIMADYCYVQ
VAVLLSLNNSQRRIRIITLAMPTTESLAEVYASADQLAIASFYNSKAVEKALNSSLDDAR
VLINKSVQDILATYKKEIVVSNTAGGAPLRLCANLRMFPLLMHSLTKHMAFRSGIVPSDH
RASALNNLESLPLKYLIKNIYPDVYSLHDMADEAGLPVQTEDGEATGTIVLPQPINATSS
LFERYGLYLIDNGNELFLWMGGDAVPALVFDVFGTQDIFDIPIGKQEIPVVENSEFNQRV
RNIINQLRNHDDVITYQSLYIVRGASLSEPVNHASAREVATLRLWASSTLVEDKILNNES
YREFLQIMKARISK

Sequence of entity 3 (B), FASTA

>6GNI_3 Small COPII coat GTPase SAR1 (chains B)
HGKLLFLGLDNAGKTTLLHMLKNDRLATLQPTWHPTSEELAIGNIKFTTFDLGGHIQARR
LWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAELKDVPFVILGNKIDAPNAVSE
AELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYLEAFQWLSQY

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1
ZN	Zinc ion	Zn	2

Primary citation

Subtomogram averaging of COPII assemblies reveals how coat organization dictates membrane shape. Hutchings, J., Stancheva, V., Miller, E.A. et al. Nat Commun (2018) 9:4154-4154. DOI 10.1038/s41467-018-06577-4 · 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
6ZGA 4.6 Å, COPII on membranes, inner coat
4BZI 23.0 Å, The structure of the COPII coat assembled on membranes

Browse structure collections

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