8HQX: Coatomer subunit beta'

The complex structure of COPI cargo sorting module with TAT-WDM peptide. Determined by X-ray diffraction at 1.54 Å resolution. Released 20 Dec 2023.

Method: X-ray diffraction
Resolution: 1.54 Å
Organisms: Saccharomyces cerevisiae (strain YJM789), Homo sapiens
Chains: 2
Atoms: 2,513
Mol. weight: 34.97 kDa
Released: 20 Dec 2023

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

Secondary structure: helices and β-sheets

8HQX contains 2 α-helices and 28 β-strands across 1 chain. 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: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	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	120-125	6	4
α-helix	126-128	3
β-strand	131-137	7	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
β-strand	287-291	5	1
β-strand	294-299	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coatomer subunit beta'	A	protein	301	Saccharomyces cerevisiae (strain YJM789)	P41811 (AlphaFold model)
TAT-WDM KxKxx motif	B	protein	6	Homo sapiens

Sequence of entity 1 (A), FASTA

>8HQX_1 Coatomer subunit beta' (chains A)
MKLDIKKTFSNRSDRVKGIDFHPTEPWVLTTLYSGRVEIWNYETQVEVRSIQVTETPVRA
GKFIARKNWIIVGSDDFRIRVFNYNTGEKVVDFEAHPDYIRSIAVHPTKPYVLSGSDDLT
VKLWNWENNWALEQTFEGHEHFVMCVAFNPKDPSTFASGCLDRTVKVWSLGQSTPNFTLT
TGQERGVNYVDYYPLPDKPYMITASDDLTIKIWDYQTKSCVATLEGHMSNVSFAVFHPTL
PIIISGSEDGTLKIWNSSTYKVEKTLNVGLERSWCIATHPTGRKNYIASGFDNGFTVLSL
G

Sequence of entity 2 (B), FASTA

>8HQX_2 TAT-WDM KxKxx motif (chains B)
AKEKSD

Primary citation

SARS-CoV-2 spike host cell surface exposure promoted by a COPI sorting inhibitor. Li, Y., Yang, M., Nan, Y. et al. Acta Pharm Sin B (2023) 13:3043-3053. DOI 10.1016/j.apsb.2023.04.007 · 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…
8ENW 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike…
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
4J79 1.56 Å, Crystal structure of beta'-COP/PEDVspike complex

Browse structure collections

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