4J86: Beta'-COP/yWbp1 complex

Crystal structure of beta'-COP/yWbp1 complex. Determined by X-ray diffraction at 1.48 Å resolution. Released 27 Mar 2013.

Method: X-ray diffraction
Resolution: 1.48 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 5,618
Mol. weight: 70.07 kDa
Released: 27 Mar 2013

Explore 4J86 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4J86 contains 10 α-helices and 56 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: 4 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
α-helix	126-128	3
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	220-225	6	6
β-strand	231-236	6	7
β-strand	242-247	6	7
β-strand	251-256	6	7
β-strand	262-267	6	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	6-12	7	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	286-291	6	8
β-strand	294-299	6	8

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coatomer subunit beta'	A, B	protein	301	Saccharomyces cerevisiae	P41811 (AlphaFold model)
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1	C, D	protein	6	Saccharomyces cerevisiae	P33767 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4J86_1 Coatomer subunit beta' (chains A, B)
MKLDIKKTFSNRSDRVKGIDFHPTEPWVLTTLYSGRVEIWNYETQVEVRSIQVTETPVRA
GKFIARKNWIIVGSDDFRIRVFNYNTGEKVVDFEAHPDYIRSIAVHPTKPYVLSGSDDLT
VKLWNWENNWALEQTFEGHEHFVMCVAFNPKDPSTFASGCLDRTVKVWSLGQSTPNFTLT
TGQERGVNYVDYYPLPDKPYMITASDDLTIKIWDYQTKSCVATLEGHMSNVSFAVFHPTL
PIIISGSEDGTLKIWNSSTYKVEKTLNVGLERSWCIATHPTGRKNYIASGFDNGFTVLSL
G

Sequence of entity 2 (C, D), FASTA

>4J86_2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 (chains C, D)
TFKKTN

Primary citation

Rules for the recognition of dilysine retrieval motifs by coatomer. Ma, W., Goldberg, J. EMBO J (2013) 32:926-937. DOI 10.1038/emboj.2013.41 · 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
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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