6ZG5: Protein transport protein SEC31

Name: PDB 6ZG5: COPII on membranes, outer coat right-handed rod, class1
Published: 2021-02-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: protein transport

COPII on membranes, outer coat right-handed rod, class1. Determined by electron microscopy at 40.0 Å resolution. Released 17 Feb 2021.

Method: Electron microscopy
Resolution: 40.0 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 9,971
Mol. weight: 343.94 kDa
Released: 17 Feb 2021

Explore 6ZG5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZG5 contains 53 α-helices and 71 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: 22 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	385-387	3	1
α-helix	388-390	3
β-strand	391-395	5	1
β-strand	402-405	4	1
α-helix	416-424	9
α-helix	428-436	9
α-helix	441-456	16
α-helix	458-466	9
β-strand	504	1	2
α-helix	509-519	11
α-helix	523-531	9
α-helix	536-543	8
α-helix	551-554	4
α-helix	556-560	5
α-helix	568-577	10
α-helix	582-587	6
β-strand	588	1	3
α-helix	590-592	3
α-helix	593-603	11
α-helix	608-623	16
α-helix	628-638	11
α-helix	641-650	10
α-helix	652-660	9
α-helix	666-685	20
α-helix	697-711	15
α-helix	716-725	10
α-helix	731-744	14

Chain B: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
α-helix	11	1
β-strand	12-15	4	4
β-strand	23-28	6	4
β-strand	32-38	7	4
β-strand	43-50	8	4
β-strand	56-61	6	5
α-helix	62-63	2
β-strand	65	1	6
β-strand	67	1	6
β-strand	69-74	6	5
β-strand	78-85	8	5
β-strand	88-95	8	5
β-strand	102-107	6	7
β-strand	116-120	5	7
β-strand	124-128	5	7
β-strand	139-142	4	7
β-strand	148-153	6	8
α-helix	154-156	3
β-strand	172-177	6	8
β-strand	182-188	7	8
α-helix	189-191	3
β-strand	193-200	8	8
β-strand	207-212	6	9
β-strand	220-226	7	9
β-strand	231-236	6	9
β-strand	244-247	4	9
α-helix	252-253	2
β-strand	259-262	4	10
β-strand	269-272	4	10
β-strand	278-283	6	10
β-strand	289-291	3	10

Chain C: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	385-387	3	11
β-strand	391-395	5	11
β-strand	402-405	4	11
β-strand	409	1	12
β-strand	412	1	12
α-helix	416-424	9
α-helix	428-436	9
α-helix	441-455	15
α-helix	457-466	10
β-strand	504	1	3
α-helix	509-519	11
α-helix	523-532	10
α-helix	536-543	8
α-helix	549-552	4
α-helix	554-563	10
α-helix	568-577	10
α-helix	582-586	5
β-strand	588	1	2
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	652-661	10
α-helix	666-687	22
α-helix	697-712	16
α-helix	716-723	8
α-helix	731-744	14

Chain F: 5 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	11
α-helix	11	1
β-strand	12-15	4	13
β-strand	25-28	4	13
β-strand	32-39	8	13
β-strand	42-50	9	13
β-strand	56-61	6	14
α-helix	62-63	2
α-helix	64-66	3
β-strand	69-74	6	14
β-strand	79-83	5	14
α-helix	85-87	3
β-strand	90-95	6	14
β-strand	102-107	6	15
α-helix	108-109	2
β-strand	115-120	6	15
β-strand	124-129	6	15
β-strand	139-142	4	15
β-strand	148-150	3	16
β-strand	153	1	16
β-strand	172-177	6	16
β-strand	182-186	5	16
β-strand	195-196	2	16
β-strand	209-212	4	17
β-strand	220	1	18
β-strand	222-226	5	17
β-strand	230-231	2	17
β-strand	232	1	19
β-strand	235	1	20
β-strand	236	1	18
β-strand	244	1	20
β-strand	247	1	19
β-strand	259-262	4	21
β-strand	269-272	4	21
β-strand	278-281	4	21
β-strand	282	1	22
β-strand	290	1	22

Molecules and chains

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

Sequence of entity 1 (A, C), FASTA

>6ZG5_1 Protein transport protein SEC31 (chains A, C)
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), FASTA

>6ZG5_2 Protein transport protein SEC13 (chains B)
MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVD
WAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVAS
SDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADN
LVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQ
GPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

Sequence of entity 3 (F), FASTA

>6ZG5_3 Protein transport protein SEC13 (chains F)
MVVIANAHNEMIHDAVMDYYGKRMATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVD
WAHPKFGTILASCSYDGKVMIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPMLLVAS
SDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADN
LVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYMASVSQDRTCIIWTQDNEQ
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
6ZG6 12.0 Å, COPII on membranes, outer coat vertex
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
6ZL0 40.0 Å, COPII on membranes, outer coat left-handed rod

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