1M2V: Yeast Sec23/24 heterodimer

Crystal Structure of the yeast Sec23/24 heterodimer. Determined by X-ray diffraction at 2.75 Å resolution. Released 20 Sept 2002.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 11,577
Mol. weight: 189.33 kDa
Ligands: ZN
Released: 20 Sept 2002

Explore 1M2V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1M2V contains 72 α-helices and 80 β-strands across 2 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, 41 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	12-14	3	1
β-strand	16	1	2
β-strand	19-20	2	3
α-helix	23-28	6
β-strand	33-37	5	1
β-strand	48-49	2	4
β-strand	55	1	5
β-strand	64	1	5
β-strand	70-72	3	6
β-strand	77-79	3	6
β-strand	86-88	3	6
α-helix	91-93	3
α-helix	103-105	3
β-strand	109-113	5	4
β-strand	123-129	7	7
α-helix	134-148	15
α-helix	155	1
β-strand	156-162	7	7
β-strand	165-170	6	7
β-strand	178-183	6	7
α-helix	190-197	8
α-helix	224-226	3
β-strand	229-230	2	7
α-helix	232-234	3
α-helix	235-243	9
β-strand	256	1	8
α-helix	257-259	3
α-helix	262-277	16
β-strand	282-288	7	7
β-strand	303	1	8
α-helix	307-309	3
α-helix	311-315	5
α-helix	322-339	18
β-strand	342-348	7	7
α-helix	355-364	10
β-strand	369-372	4	7
α-helix	378-386	9
β-strand	390	1	9
β-strand	396	1	9
β-strand	399-408	10	4
β-strand	413-418	6	1
β-strand	422-423	2	4
β-strand	432	1	1
β-strand	439	1	1
β-strand	444-450	7	4
β-strand	456-461	6	1
β-strand	484-494	11	4
β-strand	500-510	11	4
β-strand	511-512	2	3
α-helix	517-521	5
β-strand	523	1	2
α-helix	525-541	17
α-helix	548-563	16
β-strand	565-567	3	10
β-strand	570-575	6	10
α-helix	583-590	8
α-helix	603-613	11
α-helix	618-625	8
β-strand	628-632	5	11
β-strand	639-640	2	11
α-helix	645-647	3
β-strand	653-657	5	11
β-strand	661-666	6	11
α-helix	667	1
α-helix	668-674	7
α-helix	678-680	3
α-helix	682-684	3
α-helix	685-702	18
α-helix	708-709	2
β-strand	710-715	6	11
α-helix	721-725	5
α-helix	752-763	12

Chain B: 40 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	64-72	9
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	7
α-helix	314-318	5
α-helix	321-331	11
β-strand	344-345	2	20
β-strand	347-350	4	7
β-strand	354-358	5	7
β-strand	374-378	5	7
β-strand	394-395	2	20
α-helix	400-413	14
α-helix	424-435	12
β-strand	440-446	7	7
α-helix	471	1
α-helix	472-476	5
α-helix	482-493	12
β-strand	495-503	9	7
α-helix	509-517	9
β-strand	523-527	5	7
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	768	Saccharomyces cerevisiae	P15303 (AlphaFold model)
protein transport protein SEC24	B	protein	926	Saccharomyces cerevisiae	P40482 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1M2V_1 protein transport protein SEC23 (chains A)
MDFETNEDINGVRFTWNVFPSTRSDANSNVVPVGCLYTPLKEYDELNVAPYNPVVCSGPH
CKSILNPYCVIDPRNSSWSCPICNSRNHLPPQYTNLSQENMPLELQSTTIEYITNKPVTV
PPIFFFVVDLTSETENLDSLKESIITSLSLLPPNALIGLITYGNVVQLHDLSSETIDRCN
VFRGDREYQLEALTEMLTGQKPTGPGGAASHLPNAMNKVTPFSLNRFFLPLEQVEFKLNQ
LLENLSPDQWSVPAGHRPLRATGSALNIASLLLQGCYKNIPARIILFASGPGTVAPGLIV
NSELKDPLRSHHDIDSDHAQHYKKACKFYNQIAQRVAANGHTVDIFAGCYDQIGMSEMKQ
LTDSTGGVLLLTDAFSTAIFKQSYLRLFAKDEEGYLKMAFNGNMAVKTSKDLKVQGLIGH
ASAVKKTDANNISESEIGIGATSTWKMASLSPYHSYAIFFEIANTAANSNPMMSAPGSAD
RPHLAYTQFITTYQHSSGTNRIRVTTVANQLLPFGTPAIAASFDQEAAAVLMARIAVHKA
ETDDGADVIRWLDRTLIKLCQKYADYNKDDPQSFRLAPNFSLYPQFTYYLRRSQFLSVFN
NSPDETAFYRHIFTREDTTNSLIMIQPTLTSFSMEDDPQPVLLDSISVKPNTILLLDTFF
FILIYHGEQIAQWRKAGYQDDPQYADFKALLEEPKLEAAELLVDRFPLPRFIDTEAGGSQ
ARFLLSKLNPSDNYQDMARGGSTIVLTDDVSLQNFMTHLQQVAVSGQA

Sequence of entity 2 (B), FASTA

>1M2V_2 protein transport protein SEC24 (chains B)
MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ
FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA
YGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPD
YIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPLNEDGLIVRCRRCRSYMNP
FVTFIEQGRRWRCNFCRLANDVPMQMDQSDPNDPKSRYDRNEIKCAVMEYMAPKEYTLRQ
PPPATYCFLIDVSQSSIKSGLLATTINTLLQNLDSIPNHDERTRISILCVDNAIHYFKIP
LDSENNEESADQINMMDIADLEEPFLPRPNSMVVSLKACRQNIETLLTKIPQIFQSNLIT
NFALGPALKSAYHLIGGVGGKIIVVSGTLPNLGIGKLQRRNESGVVNTSKETAQLLSCQD
SFYKNFTIDCSKVQITVDLFLASEDYMDVASLSNLSRFTAGQTHFYPGFSGKNPNDIVKF
STEFAKHISMDFCMETVMRARGSTGLRMSRFYGHFFNRSSDLCAFSTMPRDQSYLFEVNV
DESIMADYCYVQVAVLLSLNNSQRRIRIITLAMPTTESLAEVYASADQLAIASFYNSKAV
EKALNSSLDDARVLINKSVQDILATYKKEIVVSNTAGGAPLRLCANLRMFPLLMHSLTKH
MAFRSGIVPSDHRASALNNLESLPLKYLIKNIYPDVYSLHDMADEAGLPVQTEDGEATGT
IVLPQPINATSSLFERYGLYLIDNGNELFLWMGGDAVPALVFDVFGTQDIFDIPIGKQEI
PVVENSEFNQRVRNIINQLRNHDDVITYQSLYIVRGASLSEPVNHASAREVATLRLWASS
TLVEDKILNNESYREFLQIMKARISK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structure of the Sec23/24-Sar1 pre-budding complex of the COPII vesicle coat. Bi, X., Corpina, R.A., Goldberg, J. Nature (2002) 419:271-277. DOI 10.1038/nature01040 · 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
8BSH 3.8 Å, COPII inner coat
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

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