8WYS: Local map of human CD5L

Local map of human CD5L bound to IgM-Fc/J. Determined by electron microscopy at 3.41 Å resolution. Released 9 Oct 2024.

Method: Electron microscopy
Resolution: 3.41 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,340
Mol. weight: 148.08 kDa
Ligands: CA, NAG
Released: 9 Oct 2024

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

Secondary structure: helices and β-sheets

8WYS contains 28 α-helices and 76 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: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	346-347	2	1
α-helix	354-358	5
β-strand	363-364	2	2
β-strand	369-370	2	1
β-strand	379	1	3
β-strand	382-383	2	4
β-strand	389	1	4
β-strand	395	1	5
β-strand	407	1	1
β-strand	408	1	5
β-strand	412-413	2	2
α-helix	415-418	4
β-strand	424	1	6
β-strand	425-426	2	4
β-strand	427-428	2	7
β-strand	429	1	3
β-strand	437-438	2	7
β-strand	441	1	6
β-strand	453-457	5	8
α-helix	458-460	3
α-helix	461-464	4
β-strand	469-477	9	8
β-strand	485-490	6	9
β-strand	493-494	2	9
α-helix	495-496	2
β-strand	500-502	3	8
β-strand	506-507	2	8
α-helix	508	1
β-strand	515-524	10	8
α-helix	525-528	4
β-strand	534-539	6	9
β-strand	547-552	6	9
α-helix	554-557	4
β-strand	565-568	4	10

Chain J: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	15
β-strand	15-19	5	15
β-strand	21-22	2	22
β-strand	32-33	2	22
β-strand	34-42	9	15
β-strand	46	1	23
α-helix	55	1
β-strand	56	1	23
α-helix	57	1
β-strand	59-62	4	10
α-helix	64-67	4
α-helix	73	1
β-strand	74-77	4	24
β-strand	81	1	16
β-strand	82-85	4	24
β-strand	86	1	14
β-strand	110-115	6	25
β-strand	122-127	6	25
α-helix	130-133	4

Chain L: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	346-347	2	11
α-helix	350-352	3
β-strand	365-370	6	11
β-strand	382-383	2	12
β-strand	389	1	12
β-strand	393-396	4	11
α-helix	397	1
β-strand	407-411	5	11
α-helix	415-420	6
β-strand	424-428	5	12
β-strand	437-441	5	12
β-strand	453-457	5	13
α-helix	458-460	3
α-helix	461-464	4
β-strand	470-479	10	13
β-strand	485-490	6	14
β-strand	493-494	2	14
α-helix	495-496	2
β-strand	500-502	3	13
α-helix	503-504	2
β-strand	506-507	2	13
α-helix	508	1
β-strand	515-517	3	13
β-strand	519-523	5	13
α-helix	525-528	4
β-strand	534-539	6	14
β-strand	547-552	6	14
β-strand	561-569	9	15

Chain M: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	140-141	2	16
β-strand	148-151	4	16
β-strand	152-155	4	17
β-strand	158-161	4	17
α-helix	169-179	11
β-strand	184-190	7	16
α-helix	199-200	2
β-strand	201	1	17
β-strand	233-238	6	16
α-helix	239-242	4
β-strand	243-248	6	18
β-strand	254-260	7	18
β-strand	265-267	3	18
β-strand	268	1	19
β-strand	269	1	20
α-helix	275-284	10
α-helix	296-299	4
β-strand	310	1	19
β-strand	314	1	21
β-strand	326	1	21
α-helix	337-339	3
β-strand	340	1	20
β-strand	342-344	3	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu	A, L	protein	403	Homo sapiens	P01871 (AlphaFold model), P60568 (AlphaFold model)
Interleukin-2,CD5 antigen-like	M	protein	359	Homo sapiens	O43866 (AlphaFold model), P60568 (AlphaFold model)
Immunoglobulin J chain	J	protein	168	Homo sapiens	P01591 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>8WYS_1 Interleukin-2,Isoform 1 of Immunoglobulin heavy constant mu (chains A, L)
MYRMQLLSCIALSLALVTNSASAWSHPQFEKGGGSGGGSGGSAWSHPQFEKIDTTIAELP
PKVSVFVPPRDGFFGNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKE
SGPTTYKVTSTLTIKESDWLGQSMFTCRVDHRGLTFQQNASSMCVPDQDTAIRVFAIPPS
FASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNATFSAVGEASI
CEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGVALHRPDVYLLPPAREQLNLRESATIT
CLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRYFAHSILTVSEEEWNTGET
YTCVVAHEALPNRVTERTVDKSTGKPTLYNVSLVMSDTAGTCY

Sequence of entity 2 (M), FASTA

>8WYS_2 Interleukin-2,CD5 antigen-like (chains M)
MYRMQLLSCIALSLALVTNSARIHHHHHHHHSPSGVRLVGGLHRCEGRVEVEQKGQWGTV
CDDGWDIKDVAVLCRELGCGAASGTPSGILYEPPAEKEQKVLIQSVSCTGTEDTLAQCEQ
EEVYDCSHDEDAGASCENPESSFSPVPEGVRLADGPGHCKGRVEVKHQNQWYTVCQTGWS
LRAAKVVCRQLGCGRAVLTQKRCNKHAYGRKPIWLSQMSCSGREATLQDCPSGPWGKNTC
NHDEDTWVECEDPFDLRLVGGDNLCSGRLEVLHKGVWGSVCDDNWGEKEDQVVCKQLGCG
KSLSPSFRDRKCYGPGVGRIWLDNVRCSGEEQSLEQCQHRFWGFHDCTHQEDVAVICSG

Sequence of entity 3 (J), FASTA

>8WYS_3 Immunoglobulin J chain (chains J)
MKNHLLFWGVLAVFIKAVHVKAQEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNI
RIIVPLNNRENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSAT
ETCYTYDRNKCYTAVVPLVYGGETKMVETALTPDACYPDYPYDVPDYA

Ligands and cofactors

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

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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