3MZK: Sec13/Sec16 complex, S.cerevisiae

Sec13/Sec16 complex, S.cerevisiae. Determined by X-ray diffraction at 2.69 Å resolution. Released 18 Aug 2010.

Method: X-ray diffraction
Resolution: 2.69 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 10,662
Mol. weight: 165.98 kDa
Released: 18 Aug 2010

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

Secondary structure: helices and β-sheets

3MZK contains 53 α-helices and 64 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: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	12-17	6	2
β-strand	23-28	6	2
β-strand	32-39	8	2
β-strand	42-50	9	2
β-strand	56-61	6	3
α-helix	62-63	2
α-helix	64-66	3
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	110-112	3
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	157-161	5	6
α-helix	162-164	3
β-strand	166-170	5	6
β-strand	172-177	6	5
β-strand	182-188	7	5
β-strand	193-200	8	5
β-strand	207-212	6	7
β-strand	220-226	7	7
β-strand	231-236	6	7
β-strand	244-247	4	7
β-strand	257-262	6	8
β-strand	269-273	5	8
β-strand	278-283	6	8
β-strand	289-295	7	8

Chain B: 23 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	995-998	4	1
β-strand	1003-1007	5	1
β-strand	1027-1031	5	1
α-helix	1032-1034	3
α-helix	1040-1044	5
α-helix	1056-1073	18
α-helix	1080-1090	11
α-helix	1095-1102	8
α-helix	1106-1113	8
β-strand	1125	1	9
α-helix	1130-1141	12
α-helix	1145-1154	10
α-helix	1158-1166	9
α-helix	1170-1182	13
α-helix	1193-1205	13
α-helix	1210-1219	10
α-helix	1221-1229	9
α-helix	1231-1240	10
α-helix	1243-1244	2
α-helix	1254-1269	16
α-helix	1273-1282	10
α-helix	1285-1287	3
β-strand	1291	1	10
β-strand	1299	1	10
α-helix	1309-1323	15
α-helix	1332-1334	3
α-helix	1335-1347	13
α-helix	1351-1366	16
α-helix	1373-1388	16

Chain C: 21 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	995-998	4	11
β-strand	1003-1007	5	11
β-strand	1027-1031	5	11
α-helix	1032-1034	3
α-helix	1040-1044	5
α-helix	1056-1073	18
α-helix	1080-1090	11
α-helix	1095-1102	8
α-helix	1106-1113	8
β-strand	1125	1	9
α-helix	1130-1141	12
α-helix	1145-1154	10
α-helix	1158-1166	9
α-helix	1170-1182	13
α-helix	1194-1205	12
α-helix	1210-1219	10
α-helix	1221-1229	9
α-helix	1231-1240	10
α-helix	1243-1244	2
α-helix	1254-1269	16
α-helix	1273-1282	10
α-helix	1309-1323	15
α-helix	1335-1347	13
α-helix	1351-1366	16
α-helix	1373-1388	16

Chain D: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	11
β-strand	12-17	6	12
β-strand	23-28	6	12
β-strand	32-39	8	12
β-strand	42-50	9	12
β-strand	56-61	6	13
α-helix	62-63	2
α-helix	64-66	3
β-strand	69-74	6	13
β-strand	79-85	7	13
β-strand	88-95	8	13
β-strand	102-107	6	14
α-helix	110-112	3
β-strand	115-120	6	14
β-strand	124-129	6	14
β-strand	139-142	4	14
β-strand	148-153	6	15
α-helix	154-156	3
β-strand	157-161	5	16
β-strand	166-170	5	16
β-strand	172-177	6	15
β-strand	182-188	7	15
β-strand	193-200	8	15
β-strand	207-212	6	17
β-strand	220-226	7	17
β-strand	231-236	6	17
β-strand	244-247	4	17
β-strand	257-262	6	18
β-strand	269-273	5	18
β-strand	278-283	6	18
β-strand	289-295	7	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein transport protein SEC13	A, D	protein	297	Saccharomyces cerevisiae	Q04491 (AlphaFold model)
Protein transport protein SEC16	B, C	protein	441	Saccharomyces cerevisiae	P48415 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>3MZK_1 Protein transport protein SEC13 (chains A, D)
MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVD
WAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVAS
SDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADN
LVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQ
GPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

Sequence of entity 2 (B, C), FASTA

>3MZK_2 Protein transport protein SEC16 (chains B, C)
GPGSDNEALLRRQFPIFHWSAANKVVYAVPPIPDQSQYMISSSIVQEIKVTPIDQIIKPN
DMLKSFPGPLGSAKLKKKDLTKWMETTIKSISENESSTDMTIWQLLEMKLNDKVNWKNIS
KLLYNSDELLMYLSQPFPNGDMIPNAYRLDINCQMRVLAFLQTGNHDEALRLALSKRDYA
IALLVGSLMGKDRWSEVIQKYLYEGFTAGPNDQKELAHFLLLIFQVFVGNSKMAIKSFYT
NNETSQWASENWKSIVAAVLINIPENNEDPLLIPPVVLEFLIEFGIFLTKKGLTAAASTL
FIIGNVPLSNEPVMADSDVIFESIGNMNTFESILWDEIYEYIFSYDPKFKGFSSILPQKI
YHASLLQEQGLNSLGTKYTDYLSSSVRKLPKKDILTINLTRELSEVASRLSESNTGWLAK
PKLSSVWGQLDKSFNKYIGGD

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
3MZL 2.8 Å, Sec13/Sec31 edge element, loop deletion mutant
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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