8R8B: Coatomer subunit beta'

Wnt binding to COPalpha and COPBeta2 directs secretion on extracellular vesicles. Determined by X-ray diffraction at 1.81 Å resolution. Released 13 Nov 2024.

Method: X-ray diffraction
Resolution: 1.81 Å
Organism: Saccharomyces cerevisiae
Chains: 48
Atoms: 64,338
Mol. weight: 874.18 kDa
Released: 13 Nov 2024

Explore 8R8B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R8B contains 65 α-helices and 672 β-strands across 24 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 AAA and CCC: 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	143-149	7	5
β-strand	152-160	9	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	210-214	5	6
β-strand	219-224	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 BBB: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	8
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
β-strand	131-136	6	11
β-strand	143-149	7	12
β-strand	152-160	9	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	210-214	5	13
β-strand	219-224	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	294-299	6	8

Chain DDD: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	22
β-strand	16-21	6	23
β-strand	27-32	6	23
β-strand	36-41	6	23
β-strand	46-52	7	23
β-strand	60-64	5	24
α-helix	65-67	3
β-strand	69-73	5	24
β-strand	78-83	6	24
β-strand	89-94	6	24
β-strand	100-105	6	25
β-strand	111-116	6	25
β-strand	120-125	6	25
α-helix	126-128	3
β-strand	131-137	7	25
β-strand	143-149	7	26
β-strand	152-160	9	26
β-strand	164-169	6	26
β-strand	177-180	4	26
β-strand	189-192	4	27
β-strand	200-204	5	27
β-strand	209-214	6	27
β-strand	219-225	7	27
β-strand	231-236	6	28
β-strand	242-247	6	28
β-strand	252-256	5	28
β-strand	262-266	5	28
β-strand	273-278	6	22
α-helix	283-285	3
β-strand	286-291	6	22
β-strand	294-299	6	22

Chain EEE: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	29
β-strand	16-21	6	30
β-strand	27-32	6	30
β-strand	36-41	6	30
β-strand	47-52	6	30
β-strand	58-64	7	31
α-helix	65-67	3
β-strand	69-74	6	31
β-strand	78-83	6	31
β-strand	89-94	6	31
β-strand	100-105	6	32
β-strand	111-116	6	32
β-strand	121-125	5	32
α-helix	126-128	3
β-strand	131-136	6	32
β-strand	143-149	7	33
β-strand	152-160	9	33
β-strand	164-169	6	33
β-strand	177-180	4	33
β-strand	189-192	4	34
β-strand	200-204	5	34
β-strand	209-214	6	34
β-strand	219-225	7	34
β-strand	231-236	6	35
β-strand	242-247	6	35
β-strand	252-256	5	35
β-strand	262-266	5	35
β-strand	273-278	6	29
α-helix	283-285	3
β-strand	287-291	5	29
β-strand	294-299	6	29

Chain FFF: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	36
β-strand	16-21	6	37
β-strand	27-32	6	37
β-strand	36-41	6	37
β-strand	46-52	7	37
β-strand	60-64	5	38
β-strand	69-73	5	38
β-strand	78-83	6	38
β-strand	89-94	6	38
β-strand	100-105	6	39
β-strand	111-116	6	39
β-strand	120-125	6	39
β-strand	131-137	7	39
β-strand	143-149	7	40
β-strand	152-160	9	40
β-strand	164-169	6	40
β-strand	177-180	4	40
β-strand	189-192	4	41
β-strand	200-204	5	41
β-strand	209-214	6	41
β-strand	219-225	7	41
β-strand	231-236	6	42
β-strand	242-247	6	42
β-strand	251-256	6	42
β-strand	262-267	6	42
β-strand	273-278	6	36
α-helix	283-285	3
β-strand	287-291	5	36
β-strand	294-300	7	36

Chain GGG: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	43
β-strand	16-21	6	44
β-strand	27-32	6	44
β-strand	36-41	6	44
β-strand	47-52	6	44
β-strand	58-64	7	45
α-helix	65-67	3
β-strand	69-74	6	45
β-strand	78-83	6	45
β-strand	89-94	6	45
β-strand	100-105	6	46
β-strand	111-116	6	46
β-strand	121-125	5	46
α-helix	126-128	3
β-strand	131-136	6	46
β-strand	143-149	7	47
β-strand	152-160	9	47
β-strand	164-169	6	47
β-strand	177-180	4	47
β-strand	187-192	6	48
β-strand	200-205	6	48
β-strand	209-214	6	48
β-strand	219-225	7	48
β-strand	231-236	6	49
β-strand	242-247	6	49
β-strand	252-256	5	49
β-strand	262-266	5	49
β-strand	273-278	6	43
α-helix	283-285	3
β-strand	286-291	6	43
β-strand	294-299	6	43

Chain HHH: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	50
β-strand	16-21	6	51
β-strand	27-32	6	51
β-strand	36-41	6	51
β-strand	46-52	7	51
β-strand	58-64	7	52
β-strand	69-74	6	52
β-strand	78-83	6	52
β-strand	89-94	6	52
β-strand	100-105	6	53
β-strand	111-116	6	53
β-strand	121-125	5	53
α-helix	126-128	3
β-strand	131-136	6	53
β-strand	143-149	7	54
β-strand	152-160	9	54
β-strand	164-169	6	54
β-strand	177-180	4	54
β-strand	189-192	4	55
β-strand	200-204	5	55
β-strand	210-214	5	55
β-strand	219-224	6	55
β-strand	231-236	6	56
β-strand	242-247	6	56
β-strand	252-256	5	56
β-strand	262-266	5	56
β-strand	273-278	6	50
α-helix	283-285	3
β-strand	287-291	5	50
β-strand	294-299	6	50

Chain III: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	57
β-strand	16-21	6	58
β-strand	27-32	6	58
β-strand	36-41	6	58
β-strand	47-52	6	58
β-strand	58-64	7	59
α-helix	65-67	3
β-strand	69-74	6	59
β-strand	78-83	6	59
β-strand	89-94	6	59
β-strand	100-105	6	60
β-strand	111-116	6	60
β-strand	121-125	5	60
α-helix	126-128	3
β-strand	131-136	6	60
β-strand	143-148	6	61
β-strand	155-160	6	61
β-strand	164-169	6	61
β-strand	177-180	4	61
β-strand	187-192	6	62
β-strand	200-205	6	62
β-strand	209-214	6	62
β-strand	219-225	7	62
β-strand	231-236	6	63
β-strand	242-247	6	63
β-strand	252-256	5	63
β-strand	262-266	5	63
β-strand	273-278	6	57
α-helix	283-285	3
β-strand	287-291	5	57
β-strand	294-299	6	57

15 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coatomer subunit beta'	AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ, KKK, LLL, MMM, NNN, OOO, PPP, QQQ, RRR, SSS, TTT, UUU, VVV, WWW, XXX	protein	304	Saccharomyces cerevisiae	P41811 (AlphaFold model)
Small ribosomal subunit protein mS37	aaa, bbb, ccc, ddd, eee, fff, ggg, hhh, iii, jjj, kkk, lll, mmm, nnn, ooo, ppp, qqq, rrr, sss, ttt, uuu, vvv, www, xxx	protein	6	Saccharomyces cerevisiae	O75012 (AlphaFold model)

Sequence of entity 1 (AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ, KKK, LLL, MMM, NNN, OOO, PPP, QQQ, RRR, SSS, TTT, UUU, VVV, WWW, XXX), FASTA

>8R8B_1 Coatomer subunit beta' (chains AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ, KKK, LLL, MMM, NNN, OOO, PPP, QQQ, RRR, SSS, TTT, UUU, VVV, WWW, XXX)
MKLDIKKTFSNRSDRVKGIDFHPTEPWVLTTLYSGRVELWNYETQVEVRSIQVTETPVRA
GKFIARKNWIIVGSDDFRIRVFNYNTGEKVVDFEAHPDYIRSIAVHPTKPYVLSGSDDLT
VKLWNWENNWALEQTFEGHEHFVMCVAFNPKDPSTFASGCLDRTVKVWSLGQSTPNFTLT
TGQERGVNYVDYYPLPDKPYMITASDDLTIKIWDYQTKSCVATLEGHMSNVSFAVFHPTL
PIIISGSEDGTLKIWNSSTYKVEKTLNVGLERSWCIATHPTGRKNYIASGFDNGFTVLSL
GNDE

Sequence of entity 2 (aaa, bbb, ccc, ddd, eee, fff, ggg, hhh, iii, jjj, kkk, lll, mmm, nnn, ooo, ppp, qqq, rrr, sss, ttt, uuu, vvv, www, xxx), FASTA

>8R8B_2 Small ribosomal subunit protein mS37 (chains aaa, bbb, ccc, ddd, eee, fff, ggg, hhh, iii, jjj, kkk, lll, mmm, nnn, ooo, ppp, qqq, rrr, sss, ttt, uuu, vvv, www, xxx)
LKIKKP

Primary citation

Identification of the Wnt signal peptide that directs secretion on extracellular vesicles. Gurriaran-Rodriguez, U., Datzkiw, D., Radusky, L.G. et al. Sci Adv (2024) 10:eado5914-eado5914. DOI 10.1126/sciadv.ado5914 · 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
8HQX 1.54 Å, The complex structure of COPI cargo sorting module with TAT-WDM peptide

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