6ZG6: COPII on membranes, outer coat vertex

COPII on membranes, outer coat vertex. Determined by electron microscopy at 12.0 Å resolution. Released 17 Feb 2021.

Method: Electron microscopy
Resolution: 12.0 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 8
Atoms: 21,036
Mol. weight: 687.67 kDa
Released: 17 Feb 2021

Explore 6ZG6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZG6 contains 32 α-helices and 252 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.

Chains A, C, E and G: 3 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
β-strand	12	1	2
β-strand	15	1	3
β-strand	22-25	4	3
β-strand	26	1	2
β-strand	28	1	4
β-strand	43-46	4	3
α-helix	50-52	3
β-strand	65-70	6	4
β-strand	77-81	5	4
β-strand	86-89	4	4
β-strand	100-103	4	4
β-strand	113-116	4	5
β-strand	123	1	6
β-strand	124-127	4	5
β-strand	133-134	2	5
β-strand	135	1	7
β-strand	137	1	6
β-strand	151	1	7
β-strand	165-168	4	8
β-strand	175-179	5	8
β-strand	185-189	5	8
β-strand	194-199	6	8
α-helix	209-211	3
β-strand	212-217	6	9
β-strand	224-229	6	9
β-strand	239-241	3	9
β-strand	250	1	9
β-strand	260-265	6	10
β-strand	273-277	5	10
β-strand	281-285	5	10
β-strand	292-297	6	10
β-strand	306-308	3	1
β-strand	315-318	4	1
β-strand	324-329	6	1
β-strand	385-387	3	11
α-helix	388-390	3
β-strand	391-395	5	11
β-strand	402-405	4	11

Chains B, D, F and H: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	11
α-helix	11	1
β-strand	12-15	4	12
β-strand	23-28	6	12
β-strand	32-38	7	12
β-strand	43-50	8	12
β-strand	56-61	6	13
α-helix	62-63	2
β-strand	65	1	14
β-strand	67	1	14
β-strand	69-74	6	13
β-strand	78-85	8	13
β-strand	88-95	8	13
β-strand	102-107	6	15
β-strand	116-120	5	15
β-strand	124-128	5	15
β-strand	139-142	4	15
β-strand	148-153	6	16
α-helix	154-156	3
β-strand	172-177	6	16
β-strand	182-188	7	16
α-helix	189-191	3
β-strand	193-200	8	16
β-strand	207-212	6	17
β-strand	220-226	7	17
β-strand	231-236	6	17
β-strand	244-247	4	17
α-helix	252-253	2
β-strand	259-262	4	18
β-strand	269-272	4	18
β-strand	278-283	6	18
β-strand	289-291	3	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein transport protein SEC31	A, C, E, G	protein	1273	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38968 (AlphaFold model)
Protein transport protein SEC13	B, D, F, H	protein	297	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q04491 (AlphaFold model)

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

>6ZG6_1 Protein transport protein SEC31 (chains A, C, E, G)
MVKLAEFSRTATFAWSHDKIPLLVSGTVSGTVDANFSTDSSLELWSLLAADSEKPIASLQ
VDSKFNDLDWSHNNKIIAGALDNGSLELYSTNEANNAINSMARFSNHSSSVKTVKFNAKQ
DNVLASGGNNGEIFIWDMNKCTESPSNYTPLTPGQSMSSVDEVISLAWNQSLAHVFASAG
SSNFASIWDLKAKKEVIHLSYTSPNSGIKQQLSVVEWHPKNSTRVATATGSDNDPSILIW
DLRNANTPLQTLNQGHQKGILSLDWCHQDEHLLLSSGRDNTVLLWNPESAEQLSQFPARG
NWCFKTKFAPEAPDLFACASFDNKIEVQTLQNLTNTLDEQETETKQQESETDFWNNVSRE
ESKEKPSVFHLQAPTWYGEPSPAAHWAFGGKLVQITPDGKGVSITNPKISGLESNTTLSE
ALKTKDFKPLINQRLVKVIDDVNEEDWNLLEKLSMDGTEEFLKEALAFDNDESDAQDDAN
NEKEDDGEEFFQQIETNFQPEGDFSLSGNIEQTISKNLVSGNIKSAVKNSLENDLLMEAM
VIALDSNNERLKESVKNAYFAKYGSKSSLSRILYSISKREVDDLVENLDVSQWKFISKAI
QNLYPNDIAQRNEMLIKLGDRLKENGHRQDSLTLYLAAGSLDKVASIWLSEFPDLEDKLK
KDNKTIYEAHSECLTEFIERFTVFSNFINGSSTINNEQLIAKFLEFINLTTSTGNFELAT
EFLNSLPSDNEEVKTEKARVLIASGKSLPAQNPATATTSKAKYTNAKTNKNVPVLPTPGM
PSTTSIPSMQAPFYGMTPGASANALPPKPYVPATTTSAPVHTEGKYAPPSQPSMASPFVN
KTNSSTRLNSFAPPPNPYATATVPATNVSTTSIPQNTFAPIQPGMPIMGDYNAQSSSIPS
QPPINAVSGQTPHLNRKANDGWNDLPLKVKEKPSRAKAVSVAPPNILSTPTPLNGIPANA
ASTMPPPPLSRAPSSVSMVSPPPLHKNSRVPSLVATSESPRASISNPYAPPQSSQQFPIG
TISTANQTSNTAQVASSNPYAPPPQQRVATPLSGGVPPAPLPKASNPYAPTATTQPNGSS
YPPTGPYTNNHTMTSPPPVFNKPPTGPPPISMKKRSNKLASIEQNPSQGATYPPTLSSSA
SPLQPSQPPTLASQVNTSAENVSHEIPADQQPIVDFLKEELARVTPLTPKEYSKQLKDCD
KRLKILFYHLEKQDLLTQPTIDCLHDLVALMKEKKYKEAMVIHANIATNHAQEGGNWLTG
VKRLIGIAEATLN

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

>6ZG6_2 Protein transport protein SEC13 (chains B, D, F, H)
MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVD
WAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVAS
SDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADN
LVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQ
GPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

Primary citation

Structure of the complete, membrane-assembled COPII coat reveals a complex interaction network. Hutchings, J., Stancheva, V.G., Brown, N.R. et al. Nat Commun (2021) 12:2034-2034. DOI 10.1038/s41467-021-22110-6 · PubMed

Other PDB entries of the same protein (UniProt P38968 (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…
2QTV 2.5 Å, Structure of Sec23-Sar1 complexed with the active fragment of Sec31
3MZL 2.8 Å, Sec13/Sec31 edge element, loop deletion mutant
2PM9 3.3 Å, Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat
4BZJ 40.0 Å, The structure of the COPII coat assembled on membranes
4BZK 40.0 Å, The structure of the COPII coat assembled on membranes
6ZG5 40.0 Å, COPII on membranes, outer coat right-handed rod, class1
6ZL0 40.0 Å, COPII on membranes, outer coat left-handed rod

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