1M2O: Sec23-Sar1 complex

Crystal Structure of the Sec23-Sar1 complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 20 Sept 2002.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 14,123
Mol. weight: 215.1 kDa
Ligands: ZN, MG, GNP
Released: 20 Sept 2002

Explore 1M2O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1M2O contains 84 α-helices and 102 β-strands across 4 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: 35 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	34-37	4	1
β-strand	48-49	2	3
β-strand	55	1	4
α-helix	63	1
β-strand	64	1	4
α-helix	65	1
α-helix	70	1
β-strand	71-72	2	5
β-strand	77-78	2	5
β-strand	88	1	5
α-helix	91-93	3
α-helix	103-105	3
β-strand	109-113	5	3
β-strand	123-129	7	6
α-helix	134-149	16
β-strand	156-162	7	6
β-strand	165-168	4	6
β-strand	177-183	7	6
α-helix	190-198	9
α-helix	224-227	4
β-strand	229-230	2	6
α-helix	231-243	13
β-strand	256	1	7
α-helix	262-276	15
β-strand	283-288	6	6
β-strand	303	1	7
α-helix	307-310	4
α-helix	311-316	6
α-helix	322-339	18
β-strand	342-348	7	6
α-helix	355-365	11
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
α-helix	424-425	2
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	525-539	15
α-helix	545-563	19
β-strand	565	1	9
α-helix	571-573	3
β-strand	575	1	9
α-helix	582-592	11
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
α-helix	645-647	3
β-strand	653-657	5	10
β-strand	661-666	6	10
α-helix	668-676	9
α-helix	678-680	3
α-helix	685-703	19
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	750-751	2
α-helix	752-763	12

Chain B: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	12
α-helix	36-45	10
α-helix	51-54	4
β-strand	58-64	7	12
β-strand	67-73	7	12
α-helix	78-80	3
α-helix	84-87	4
β-strand	93-99	7	12
α-helix	103-105	3
α-helix	106-117	12
α-helix	120-122	3
α-helix	125-126	2
β-strand	127-132	6	12
α-helix	139-141	3
α-helix	142-148	7
β-strand	166-170	5	12
β-strand	172	1	13
β-strand	177	1	13
α-helix	179-187	9

Chain C: 30 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	12-14	3	14
β-strand	16	1	15
β-strand	18-20	3	16
α-helix	23-28	6
α-helix	32	1
β-strand	33-37	5	14
β-strand	48-49	2	16
β-strand	55	1	17
β-strand	64	1	17
β-strand	70-72	3	18
β-strand	77-79	3	18
β-strand	86-88	3	18
α-helix	89-90	2
α-helix	91-93	3
α-helix	103-105	3
β-strand	109-117	9	16
β-strand	123-129	7	6
α-helix	134-149	16
β-strand	156-162	7	6
β-strand	165-168	4	6
β-strand	177-183	7	6
α-helix	190-198	9
α-helix	224-227	4
β-strand	229-230	2	6
α-helix	231-243	13
β-strand	256	1	19
α-helix	262-277	16
β-strand	282-288	7	6
β-strand	303	1	19
α-helix	307-309	3
α-helix	311-315	5
α-helix	322-339	18
β-strand	341-348	8	6
α-helix	355-363	9
β-strand	369-372	4	6
α-helix	378-386	9
β-strand	390	1	20
β-strand	396	1	20
β-strand	399-408	10	16
β-strand	412-418	7	14
β-strand	422-423	2	16
β-strand	432	1	14
β-strand	439	1	14
β-strand	444-450	7	16
β-strand	456-462	7	14
β-strand	484-495	12	16
β-strand	499-512	14	16
α-helix	517-521	5
β-strand	523	1	15
α-helix	525-542	18
α-helix	545-563	19
β-strand	564-567	4	21
β-strand	570-576	7	21
α-helix	578-580	3
α-helix	583-591	9
α-helix	603-613	11
α-helix	618-625	8
β-strand	628-632	5	22
β-strand	639-640	2	22
β-strand	644	1	23
α-helix	645-647	3
β-strand	653-657	5	22
β-strand	661-666	6	22
α-helix	668-676	9
α-helix	678-680	3
α-helix	685-701	17
α-helix	708-709	2
β-strand	710-715	6	22
α-helix	722-725	4
β-strand	729	1	23
α-helix	752-763	12

Chain D: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	24
α-helix	36-44	9
β-strand	58-63	6	24
β-strand	68-73	6	24
α-helix	79-82	4
α-helix	84-87	4
β-strand	94-97	4	24
α-helix	103-105	3
α-helix	106-117	12
α-helix	120-122	3
β-strand	127	1	24
β-strand	130	1	25
α-helix	142-148	7
β-strand	166	1	24
β-strand	169	1	25
β-strand	172	1	26
β-strand	177	1	26
α-helix	179-186	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
protein transport protein SEC23	A, C	protein	768	Saccharomyces cerevisiae	P15303 (AlphaFold model)
GTP-binding protein SAR1	B, D	protein	190	Saccharomyces cerevisiae	P20606 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1M2O_1 protein transport protein SEC23 (chains A, C)
MDFETNEDINGVRFTWNVFPSTRSDANSNVVPVGCLYTPLKEYDELNVAPYNPVVCSGPH
CKSILNPYCVIDPRNSSWSCPICNSRNHLPPQYTNLSQENMPLELQSTTIEYITNKPVTV
PPIFFFVVDLTSETENLDSLKESIITSLSLLPPNALIGLITYGNVVQLHDLSSETIDRCN
VFRGDREYQLEALTEMLTGQKPTGPGGAASHLPNAMNKVTPFSLNRFFLPLEQVEFKLNQ
LLENLSPDQWSVPAGHRPLRATGSALNIASLLLQGCYKNIPARIILFASGPGTVAPGLIV
NSELKDPLRSHHDIDSDHAQHYKKACKFYNQIAQRVAANGHTVDIFAGCYDQIGMSEMKQ
LTDSTGGVLLLTDAFSTAIFKQSYLRLFAKDEEGYLKMAFNGNMAVKTSKDLKVQGLIGH
ASAVKKTDANNISESEIGIGATSTWKMASLSPYHSYAIFFEIANTAANSNPMMSAPGSAD
RPHLAYTQFITTYQHSSGTNRIRVTTVANQLLPFGTPAIAASFDQEAAAVLMARIAVHKA
ETDDGADVIRWLDRTLIKLCQKYADYNKDDPQSFRLAPNFSLYPQFTYYLRRSQFLSVFN
NSPDETAFYRHIFTREDTTNSLIMIQPTLTSFSMEDDPQPVLLDSISVKPNTILLLDTFF
FILIYHGEQIAQWRKAGYQDDPQYADFKALLEEPKLEAAELLVDRFPLPRFIDTEAGGSQ
ARFLLSKLNPSDNYQDMARGGSTIVLTDDVSLQNFMTHLQQVAVSGQA

Sequence of entity 2 (B, D), FASTA

>1M2O_2 GTP-binding protein SAR1 (chains B, D)
MAGWDIFGWFRDVLASLGLWNKHGKLLFLGLDNAGKTTLLHMLKNDRLATLQPTWHPTSE
ELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIA
ELKDVPFVILGNKIDAPNAVSEAELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYL
EAFQWLSQYI

Ligands and cofactors

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

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
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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