3MZL: Sec13/Sec31 edge element, loop deletion mutant

Sec13/Sec31 edge element, loop deletion mutant. Determined by X-ray diffraction at 2.8 Å resolution. Released 18 Aug 2010.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 19,212
Mol. weight: 287.1 kDa
Released: 18 Aug 2010

Explore 3MZL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3MZL contains 104 α-helices and 117 β-strands across 8 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: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	12-17	6	2
β-strand	23-28	6	2
β-strand	33-38	6	2
β-strand	43-49	7	2
β-strand	56-61	6	3
α-helix	62-63	2
β-strand	69-74	6	3
β-strand	79-85	7	3
β-strand	88-95	8	3
β-strand	102-107	6	4
α-helix	108-109	2
β-strand	115-120	6	4
β-strand	124-129	6	4
β-strand	139-142	4	4
β-strand	148-153	6	5
α-helix	154-156	3
β-strand	172-177	6	5
β-strand	182-188	7	5
β-strand	193-200	8	5
α-helix	201	1
β-strand	207-209	3	6
β-strand	212	1	6
β-strand	220-226	7	6
β-strand	231-236	6	6
α-helix	242-243	2
β-strand	244-247	4	6
α-helix	252-253	2
β-strand	257-262	6	7
β-strand	269-273	5	7
β-strand	278-283	6	7
β-strand	289-291	3	7

Chain B: 19 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	385-387	3	1
β-strand	391-395	5	1
β-strand	402-405	4	1
β-strand	409	1	8
β-strand	412	1	8
α-helix	416-423	8
α-helix	428-436	9
α-helix	441-456	16
α-helix	458-465	8
α-helix	509-519	11
α-helix	523-531	9
α-helix	536-544	9
α-helix	552-563	12
α-helix	568-577	10
α-helix	582-587	6
α-helix	593-603	11
α-helix	608-624	17
α-helix	628-637	10
α-helix	641-650	10
α-helix	652-656	5
α-helix	666-686	21
α-helix	697-711	15
α-helix	716-724	9
α-helix	731-744	14

Chain C: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	9
β-strand	12-17	6	10
β-strand	23-28	6	10
β-strand	32-38	7	10
β-strand	43-50	8	10
β-strand	56-61	6	11
α-helix	62-63	2
α-helix	64-66	3
β-strand	69-74	6	11
β-strand	79-85	7	11
β-strand	88-95	8	11
β-strand	102-107	6	12
α-helix	108-109	2
β-strand	115-120	6	12
β-strand	124-129	6	12
β-strand	130	1	13
β-strand	136	1	13
β-strand	139-142	4	12
β-strand	148-153	6	14
α-helix	154-156	3
β-strand	172-177	6	14
β-strand	182-188	7	14
β-strand	193-200	8	14
β-strand	207-212	6	15
β-strand	220-226	7	15
β-strand	231-236	6	15
α-helix	242-243	2
β-strand	244-247	4	15
α-helix	252-253	2
β-strand	257-262	6	16
β-strand	269-273	5	16
β-strand	278-283	6	16
β-strand	289-291	3	16

Chain D: 20 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	385-387	3	9
β-strand	391-395	5	9
β-strand	402-405	4	9
α-helix	416-423	8
α-helix	428-436	9
α-helix	441-455	15
α-helix	458-465	8
α-helix	509-519	11
α-helix	523-531	9
α-helix	536-543	8
α-helix	551-562	12
α-helix	568-577	10
α-helix	582-587	6
α-helix	590-592	3
α-helix	593-603	11
α-helix	608-624	17
α-helix	628-637	10
α-helix	641-650	10
α-helix	652-660	9
α-helix	666-685	20
α-helix	697-712	16
α-helix	716-723	8
α-helix	731-744	14

Chain E: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	17
β-strand	12-17	6	18
β-strand	24-28	5	18
β-strand	32-38	7	18
β-strand	43-50	8	18
β-strand	56-61	6	19
α-helix	62-63	2
α-helix	64-66	3
β-strand	69-74	6	19
β-strand	79-85	7	19
β-strand	88-95	8	19
β-strand	102-107	6	20
α-helix	108-109	2
α-helix	110-112	3
β-strand	115-120	6	20
β-strand	124-129	6	20
β-strand	139-142	4	20
β-strand	148-153	6	21
α-helix	154-156	3
β-strand	172-177	6	21
β-strand	182-188	7	21
β-strand	193-200	8	21
β-strand	207-212	6	22
β-strand	220-226	7	22
β-strand	231-236	6	22
α-helix	242-243	2
β-strand	244-247	4	22
α-helix	252-253	2
β-strand	257-262	6	23
β-strand	269-273	5	23
β-strand	278-283	6	23
β-strand	289-291	3	23

Chain F: 20 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	384	1
β-strand	385-387	3	17
β-strand	391-395	5	17
β-strand	402-405	4	17
α-helix	416-423	8
α-helix	428-436	9
α-helix	441-455	15
α-helix	458-465	8
α-helix	509-519	11
α-helix	523-531	9
α-helix	536-543	8
α-helix	551-562	12
α-helix	568-577	10
α-helix	582-587	6
α-helix	593-603	11
α-helix	608-625	18
α-helix	628-636	9
α-helix	641-650	10
α-helix	652-656	5
α-helix	666-685	20
α-helix	697-711	15
α-helix	716-723	8
α-helix	731-744	14

Chain G: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	24
β-strand	12-17	6	25
β-strand	23-28	6	25
β-strand	33-38	6	25
β-strand	43-49	7	25
β-strand	56-61	6	26
α-helix	62-63	2
β-strand	69-74	6	26
β-strand	79-85	7	26
β-strand	88-95	8	26
β-strand	102-107	6	27
α-helix	108-109	2
β-strand	115-120	6	27
β-strand	124-129	6	27
β-strand	139-142	4	27
β-strand	148-153	6	28
α-helix	154-156	3
β-strand	172-177	6	28
β-strand	182-188	7	28
β-strand	193-200	8	28
β-strand	207-212	6	29
β-strand	220-226	7	29
β-strand	231-236	6	29
α-helix	242-243	2
β-strand	244-247	4	29
α-helix	252-253	2
β-strand	257-262	6	30
β-strand	269-273	5	30
β-strand	278-283	6	30
β-strand	289-291	3	30

Chain H: 21 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	385-387	3	24
β-strand	391-395	5	24
β-strand	402-405	4	24
α-helix	407-409	3
α-helix	416-424	9
α-helix	428-436	9
α-helix	441-456	16
α-helix	458-465	8
α-helix	509-519	11
α-helix	523-532	10
α-helix	537-546	10
α-helix	551-560	10
α-helix	568-577	10
α-helix	581-587	7
α-helix	590-592	3
α-helix	593-603	11
α-helix	608-624	17
α-helix	628-637	10
α-helix	641-650	10
α-helix	652-660	9
α-helix	666-686	21
α-helix	697-712	16
α-helix	716-723	8
α-helix	731-744	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein transport protein SEC13	A, C, E, G	protein	297	Saccharomyces cerevisiae	Q04491 (AlphaFold model)
Protein transport protein SEC31	B, D, F, H	protein	345	Saccharomyces cerevisiae	P38968 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3MZL_1 Protein transport protein SEC13 (chains A, C, E, G)
MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVD
WAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVAS
SDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADN
LVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQ
GPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

Sequence of entity 2 (B, D, F, H), FASTA

>3MZL_2 Protein transport protein SEC31 (chains B, D, F, H)
GPHLQAPTWYGEPSPAAHWAFGGKLVQITPDGKGVSITNPKISGLESNTTLSEALKTKDF
KPLINQRLVKVIDDVNEEDWNLLEKLSMDGTEEFLKEALAFDNDESGNIEQTISKNLVSG
NIKSAVKNSLENDLLMEAMVIALDSNNERLKESVKNAYFAKYGSKSSLSRILYSISKREV
DDLVENLDVSQWKFISKAIQNLYPNDIAQRNEMLIKLGDRLKENGHRQDSLTLYLAAGSL
DKVASIWLSEFPDLEDKLKKDNKTIYEAHSECLTEFIERFTVFSNFINGSSTINNEQLIA
KFLEFINLTTSTGNFELATEFLNSLPSDNEEVKTEKARVLIASGK

Primary citation

Structure of the Sec13-Sec16 edge element, a template for assembly of the COPII vesicle coat. Whittle, J.R., Schwartz, T.U. J Cell Biol (2010) 190:347-361. DOI 10.1083/jcb.201003092 · PubMed

Other PDB entries of the same protein (UniProt Q04491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PM7 2.35 Å, Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat,…
2PM6 2.45 Å, Crystal Structure of yeast Sec13/31 edge element of the COPII vesicular coat, native…
3JRP 2.6 Å, SEC13 with NUP145C (AA109-179) insertion blade
3MZK 2.69 Å, Sec13/Sec16 complex, S.cerevisiae
8ADL 2.95 Å, Cryo-EM structure of the SEA complex
3IKO 3.2 Å, Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex
9H5K 3.2 Å, Cryo-EM structure of the SEAC-EGOC supercomplex
2PM9 3.3 Å, Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat
3JRO 4.0 Å, NUP84-NUP145C-SEC13 edge element of the NPC lattice
4XMM 7.38 Å, Structure of the yeast coat nucleoporin complex, space group C2
4XMN 7.6 Å, Structure of the yeast coat nucleoporin complex, space group P212121
8TIE 8.1 Å, Double nuclear outer ring of Nup84-complexes from the yeast NPC

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