8ENW: Beta'-COPI-WD40 domain

Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike tail heptapeptide. Determined by X-ray diffraction at 1.45 Å resolution. Released 31 Jan 2024.

Method: X-ray diffraction
Resolution: 1.45 Å
Organisms: Saccharomyces cerevisiae, Severe acute respiratory syndrome coronavirus 2
Chains: 4
Atoms: 5,546
Mol. weight: 71.14 kDa
Released: 31 Jan 2024

Explore 8ENW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ENW contains 7 α-helices and 56 β-strands across 2 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: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	1
α-helix	15	1
β-strand	16-21	6	2
β-strand	27-32	6	2
β-strand	36-41	6	2
β-strand	46-52	7	2
β-strand	58-64	7	3
α-helix	65-67	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	131-136	6	4
β-strand	143-148	6	5
β-strand	155-160	6	5
β-strand	164-169	6	5
β-strand	177-180	4	5
β-strand	189-192	4	6
β-strand	200-204	5	6
β-strand	209-214	6	6
β-strand	219-225	7	6
β-strand	231-236	6	7
β-strand	242-247	6	7
β-strand	252-256	5	7
β-strand	262-266	5	7
β-strand	273-278	6	1
α-helix	283-285	3
β-strand	287-291	5	1
β-strand	294-299	6	1

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	8
α-helix	15	1
β-strand	16-21	6	9
β-strand	27-32	6	9
β-strand	36-41	6	9
β-strand	46-52	7	9
β-strand	58-64	7	10
α-helix	65-67	3
β-strand	69-74	6	10
β-strand	78-83	6	10
β-strand	89-94	6	10
β-strand	100-105	6	11
β-strand	111-116	6	11
β-strand	121-125	5	11
α-helix	126-128	3
β-strand	131-136	6	11
β-strand	143-148	6	12
β-strand	155-160	6	12
β-strand	164-169	6	12
β-strand	177-180	4	12
β-strand	189-192	4	13
β-strand	200-204	5	13
β-strand	209-214	6	13
β-strand	220-225	6	13
β-strand	231-236	6	14
β-strand	242-247	6	14
β-strand	251-256	6	14
β-strand	262-267	6	14
β-strand	273-278	6	8
α-helix	283-285	3
β-strand	287-291	5	8
β-strand	294-300	7	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coatomer subunit beta'	A, B	protein	302	Saccharomyces cerevisiae	P41811 (AlphaFold model)
Clientized spike tail peptide	C, D	protein	7	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8ENW_1 Coatomer subunit beta' (chains A, B)
SMKLDIKKTFSNRSDRVKGIDFHPTEPWVLTTLYSGRVEIWNYETQVEVRSIQVTETPVR
AGKFIARKNWIIVGSDDFRIRVFNYNTGEKVVDFEAHPDYIRSIAVHPTKPYVLSGSDDL
TVKLWNWENNWALEQTFEGHEHFVMCVAFNPKDPSTFASGCLDRTVKVWSLGQSTPNFTL
TTGQERGVNYVDYYPLPDKPYMITASDDLTIKIWDYQTKSCVATLEGHMSNVSFAVFHPT
LPIIISGSEDGTLKIWNSSTYKVEKTLNVGLERSWCIATHPTGRKNYIASGFDNGFTVLS
LG

Sequence of entity 2 (C, D), FASTA

>8ENW_2 Clientized spike tail peptide (chains C, D)
GVKLHYE

Primary citation

A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs. Dey, D., Qing, E., He, Y. et al. Nat Commun (2023) 14:8358-8358. DOI 10.1038/s41467-023-44076-3 · PubMed

Other PDB entries of the same protein (UniProt P41811 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8EWX 1.24 Å, N-terminal WD40 domain of beta'-COPI subunit with two chains in the asymmetric unit
8F0E 1.31 Å, N-terminal WD40 domain of beta'-COPI subunit with four chains in the asymmetric unit
8HQV 1.4 Å, The complex structure of COPI cargo sorting module with HCoV-OC43 Spike KTSHxx sorting…
8HQW 1.41 Å, The complex structure of COPI cargo sorting module with MHV Spike Hxx sorting motif
4J73 1.44 Å, Crystal structure of beta'-COP/p25 complex
8ENS 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail…
4J82 1.46 Å, Crystal structure of beta'-COP/Insig-2 complex
4J84 1.47 Å, Crystal structure of beta'-COP/Scyl1 complex
4J78 1.48 Å, Crystal structure of beta'-COP/Emp47p complex
4J86 1.48 Å, Crystal structure of beta'-COP/yWbp1 complex
8HQX 1.54 Å, The complex structure of COPI cargo sorting module with TAT-WDM peptide
4J79 1.56 Å, Crystal structure of beta'-COP/PEDVspike complex

Browse structure collections

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