8WYR: Human CD5L

Cryo-EM structure of human CD5L bound to IgM-Fc/J. Determined by electron microscopy at 3.39 Å resolution. Released 9 Oct 2024.

Method: Electron microscopy
Resolution: 3.39 Å
Organism: Homo sapiens
Chains: 12
Atoms: 20,612
Mol. weight: 502.54 kDa
Ligands: CA, NAG
Released: 9 Oct 2024

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

Secondary structure: helices and β-sheets

8WYR contains 92 α-helices and 257 β-strands across 12 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: 9 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	346-347	2	1
β-strand	350	1	2
α-helix	354-355	2
α-helix	356-360	5
β-strand	363-364	2	3
β-strand	366	1	2
β-strand	368	1	4
β-strand	369-370	2	1
β-strand	373	1	5
β-strand	379-380	2	6
β-strand	383	1	7
α-helix	398	1
β-strand	399-400	2	5
β-strand	404-405	2	5
β-strand	408	1	4
β-strand	412-413	2	3
β-strand	425-426	2	7
β-strand	428-429	2	6
β-strand	439-440	2	7
α-helix	447-449	3
β-strand	453-457	5	8
α-helix	458-460	3
α-helix	461-464	4
β-strand	469-479	11	8
β-strand	485-488	4	9
β-strand	489-490	2	10
β-strand	493-494	2	10
α-helix	495-496	2
β-strand	500-502	3	8
α-helix	503-505	3
β-strand	506-507	2	8
β-strand	515-524	10	8
α-helix	525-529	5
β-strand	534-539	6	9
β-strand	547-552	6	9
β-strand	561-562	2	11
β-strand	565-569	5	12

Chain B: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	347-348	2	13
α-helix	354-360	7
β-strand	368-369	2	13
β-strand	381-382	2	14
α-helix	391-393	3
β-strand	400	1	15
β-strand	404	1	15
α-helix	415-420	6
β-strand	426-427	2	14
α-helix	443-444	2
β-strand	453-457	5	16
α-helix	458-460	3
α-helix	461-465	5
β-strand	470-479	10	16
β-strand	485-490	6	17
β-strand	493-494	2	17
α-helix	495-496	2
β-strand	500-502	3	16
α-helix	503-505	3
β-strand	506-507	2	16
β-strand	515-517	3	16
β-strand	519-523	5	16
α-helix	525-530	6
β-strand	534-539	6	17
β-strand	550-552	3	17
β-strand	561-562	2	11
β-strand	565-569	5	12

Chain C: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	346-348	3	18
α-helix	354-359	6
β-strand	363-366	4	19
β-strand	368-370	3	18
β-strand	379-383	5	20
β-strand	389-390	2	20
β-strand	407	1	18
β-strand	410-413	4	19
α-helix	415-419	5
β-strand	424-429	6	20
β-strand	437-441	5	20
α-helix	443-444	2
β-strand	456-457	2	21
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-474	5	21
β-strand	476-479	4	22
β-strand	485-487	3	23
β-strand	489-490	2	24
β-strand	493-494	2	24
α-helix	495-496	2
β-strand	500-502	3	21
α-helix	503-505	3
β-strand	506-507	2	22
β-strand	515-517	3	22
β-strand	519-523	5	21
α-helix	525-529	5
β-strand	534	1	24
β-strand	537-539	3	23
β-strand	547-548	2	23
β-strand	552	1	24
β-strand	561-562	2	11
β-strand	565-566	2	12
β-strand	568	1	25

Chain D: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	26
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-365	2	27
β-strand	366-370	5	26
β-strand	383	1	28
β-strand	411-412	2	27
α-helix	415-418	4
β-strand	424-426	3	28
β-strand	439-441	3	28
β-strand	456-457	2	29
α-helix	458-460	3
α-helix	461-464	4
β-strand	470-471	2	30
β-strand	473-474	2	29
β-strand	476-479	4	31
β-strand	485-490	6	32
β-strand	493-494	2	32
α-helix	495-496	2
β-strand	500-502	3	33
α-helix	503-504	2
β-strand	506-507	2	31
α-helix	508	1
β-strand	515-517	3	31
β-strand	519-521	3	33
β-strand	522-523	2	30
α-helix	525-529	5
β-strand	534-539	6	32
β-strand	547-552	6	32
α-helix	554-556	3
β-strand	562	1	11
β-strand	565	1	12
β-strand	568	1	25

Chain E: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	346	1	34
β-strand	349-350	2	35
α-helix	351	1
α-helix	354-359	6
β-strand	363-365	3	36
β-strand	366-367	2	35
β-strand	370	1	34
β-strand	374	1	37
β-strand	379-380	2	38
β-strand	383-384	2	39
β-strand	399	1	37
β-strand	405	1	37
β-strand	411-413	3	36
α-helix	415-420	6
β-strand	424-425	2	39
β-strand	428-429	2	38
β-strand	437	1	38
β-strand	440-441	2	39
α-helix	450-452	3
β-strand	453-457	5	40
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-479	10	40
β-strand	486-490	5	41
β-strand	493-494	2	41
β-strand	500-502	3	40
α-helix	503-505	3
β-strand	506-507	2	40
β-strand	515-523	9	40
α-helix	525-530	6
β-strand	534-538	5	41
β-strand	548-552	5	41
α-helix	554-556	3
β-strand	562	1	11
β-strand	565	1	12
β-strand	568	1	25

Chain F: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	350	1	42
α-helix	354-359	6
β-strand	363-364	2	43
β-strand	366	1	42
β-strand	381-382	2	44
β-strand	412-413	2	43
α-helix	415-420	6
β-strand	424	1	45
β-strand	426-427	2	44
β-strand	441	1	45
β-strand	453-457	5	46
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-479	10	46
β-strand	487-490	4	47
β-strand	493-494	2	47
α-helix	495-496	2
β-strand	500-502	3	46
α-helix	503-505	3
β-strand	506-507	2	46
β-strand	515-517	3	46
β-strand	519-523	5	46
α-helix	525-529	5
β-strand	534-539	6	47
β-strand	547-552	6	47
β-strand	562	1	48
β-strand	565-568	4	49

Chain G: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	346-349	4	50
α-helix	354-360	7
β-strand	363-365	3	51
β-strand	367-370	4	50
α-helix	398-399	2
β-strand	400	1	52
β-strand	404	1	52
β-strand	407	1	50
β-strand	411-413	3	51
α-helix	415-419	5
β-strand	424	1	53
β-strand	441	1	53
β-strand	453-457	5	54
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-479	10	54
β-strand	486-490	5	55
β-strand	493-494	2	55
α-helix	495-496	2
β-strand	500-502	3	54
β-strand	506-507	2	54
α-helix	508	1
β-strand	515-523	9	54
α-helix	525-530	6
β-strand	535-538	4	55
β-strand	548-550	3	55
α-helix	554-557	4
β-strand	562	1	48
β-strand	565-568	4	49

Chain H: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	347	1	56
α-helix	356-359	4
β-strand	363-364	2	57
β-strand	369	1	56
β-strand	379	1	58
β-strand	382	1	59
α-helix	388-391	4
β-strand	412-413	2	57
α-helix	416-419	4
β-strand	424-425	2	60
β-strand	426	1	59
β-strand	428	1	61
β-strand	429	1	58
β-strand	437	1	61
β-strand	440-441	2	60
β-strand	455-457	3	62
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-475	7	62
β-strand	476-479	4	63
β-strand	487-490	4	64
β-strand	493-494	2	64
α-helix	495-496	2
β-strand	500-502	3	62
α-helix	503-505	3
β-strand	506-507	2	63
β-strand	515-517	3	63
β-strand	519-524	6	62
α-helix	525-530	6
β-strand	535-539	5	64
β-strand	547-550	4	64
β-strand	562	1	48
β-strand	567	1	49

4 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
Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu	A, B, C, D, E, F, G, H, K, L	protein	403	Homo sapiens	P01871 (AlphaFold model), P60568 (AlphaFold model)
Immunoglobulin J chain	J	protein	168	Homo sapiens	P01591 (AlphaFold model)
Interleukin-2,CD5 antigen-like	M	protein	359	Homo sapiens	O43866 (AlphaFold model), P60568 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, K, L), FASTA

>8WYR_1 Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu (chains A, B, C, D, E, F, G, H, K, L)
MYRMQLLSCIALSLALVTNSASAWSHPQFEKGGGSGGGSGGSAWSHPQFEKIDTTIAELP
PKVSVFVPPRDGFFGNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKE
SGPTTYKVTSTLTIKESDWLGQSMFTCRVDHRGLTFQQNASSMCVPDQDTAIRVFAIPPS
FASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNATFSAVGEASI
CEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGVALHRPDVYLLPPAREQLNLRESATIT
CLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRYFAHSILTVSEEEWNTGET
YTCVVAHEALPNRVTERTVDKSTGKPTLYNVSLVMSDTAGTCY

Sequence of entity 2 (J), FASTA

>8WYR_2 Immunoglobulin J chain (chains J)
MKNHLLFWGVLAVFIKAVHVKAQEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNI
RIIVPLNNRENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSAT
ETCYTYDRNKCYTAVVPLVYGGETKMVETALTPDACYPDYPYDVPDYA

Sequence of entity 3 (M), FASTA

>8WYR_3 Interleukin-2,CD5 antigen-like (chains M)
MYRMQLLSCIALSLALVTNSARIHHHHHHHHSPSGVRLVGGLHRCEGRVEVEQKGQWGTV
CDDGWDIKDVAVLCRELGCGAASGTPSGILYEPPAEKEQKVLIQSVSCTGTEDTLAQCEQ
EEVYDCSHDEDAGASCENPESSFSPVPEGVRLADGPGHCKGRVEVKHQNQWYTVCQTGWS
LRAAKVVCRQLGCGRAVLTQKRCNKHAYGRKPIWLSQMSCSGREATLQDCPSGPWGKNTC
NHDEDTWVECEDPFDLRLVGGDNLCSGRLEVLHKGVWGSVCDDNWGEKEDQVVCKQLGCG
KSLSPSFRDRKCYGPGVGRIWLDNVRCSGEEQSLEQCQHRFWGFHDCTHQEDVAVICSG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

Primary citation

CD5L associates with IgM via the J chain. Wang, Y., Su, C., Ji, C. et al. Nat Commun (2024) 15:8397-8397. DOI 10.1038/s41467-024-52175-y · PubMed

Other PDB entries of the same protein (UniProt P01871 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DN0 2.28 Å, Structure of the FAB fragment from a human IgM cold agglutinin
2AGJ 2.6 Å, Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a…
1HEZ 2.7 Å, Structure of P. magnus protein L bound to a human IgM Fab.
1QLR 2.83 Å, Crystal structure of the FAB fragment of a human monoclonal IgM cold agglutinin
8BPG 3.1 Å, FcMR binding at subunit Fcu3 of IgM pentamer
9UO3 3.17 Å, Cryo-EM structure of the human IgM-Fc hexamer
7YSG 3.18 Å, Cryo-EM structure of human FcmR bound to sIgM
9UO4 3.29 Å, Cryo-EM structure of the chimeric human IgM-Fc hexamer
7K0C 3.3 Å, Structure of Secretory IgM Core
7XQ8 3.3 Å, Structure of human B-cell antigen receptor of the IgM isotype
7YG2 3.32 Å, Cryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of…
7YTC 3.39 Å, Cryo-EM structure of human FcmR bound to IgM-Fc/J

Browse structure collections

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