8R84: Pentameric IgMFc-AIM complex focused refinement

pentameric IgMFc-AIM complex focused refinement. Determined by electron microscopy at 3.6 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,470
Mol. weight: 214.77 kDa
Ligands: CA
Released: 6 Nov 2024

Explore 8R84 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R84 contains 26 α-helices and 95 β-strands across 6 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	450	1	23
β-strand	453-457	5	24
α-helix	458-460	3
α-helix	461-464	4
β-strand	469-479	11	24
β-strand	480	1	23
β-strand	485-490	6	25
β-strand	493-494	2	25
α-helix	495-496	2
β-strand	500-502	3	24
β-strand	506-507	2	24
β-strand	515-524	10	24
α-helix	525-530	6
β-strand	534-539	6	25
β-strand	547-552	6	25
β-strand	561	1	10
β-strand	564-569	6	11

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	450	1	7
β-strand	453-457	5	8
α-helix	458-460	3
α-helix	461-465	5
β-strand	470-479	10	8
β-strand	480	1	7
β-strand	485-490	6	9
β-strand	493-494	2	9
β-strand	500-502	3	8
β-strand	506-507	2	8
β-strand	515-523	9	8
α-helix	525-530	6
β-strand	534-539	6	9
β-strand	547-552	6	9
β-strand	561	1	10
β-strand	564-569	6	11

Chain J: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	17
β-strand	15-22	8	17
β-strand	32-42	11	17
β-strand	46	1	26
α-helix	55	1
β-strand	56	1	26
β-strand	60-63	4	11
β-strand	74-77	4	27
β-strand	81	1	2
β-strand	82-85	4	27
β-strand	86	1	16
β-strand	103-104	2	18
β-strand	110-113	4	25
β-strand	116-117	2	28
β-strand	120-121	2	28
β-strand	124-127	4	25

Chain K: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	450	1	19
β-strand	453-457	5	20
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-479	11	20
β-strand	480	1	19
β-strand	485-486	2	21
β-strand	489-490	2	22
β-strand	493-494	2	22
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	20
β-strand	507	1	20
β-strand	515-524	10	20
α-helix	525-529	5
β-strand	534-535	2	22
β-strand	538-539	2	21
β-strand	548	1	21
β-strand	551-552	2	22
β-strand	561	1	17
β-strand	565-567	3	17

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	12
α-helix	354-360	7
β-strand	364-372	9	12
β-strand	378-383	6	13
β-strand	389-390	2	13
β-strand	393-396	4	12
β-strand	405-412	8	12
α-helix	415-418	4
β-strand	424-430	7	13
β-strand	437-441	5	13
β-strand	450	1	14
β-strand	453-457	5	15
α-helix	458-460	3
α-helix	464-466	3
β-strand	470-479	10	15
β-strand	480	1	14
β-strand	485-490	6	16
β-strand	493-494	2	16
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	15
α-helix	503-505	3
β-strand	506-507	2	15
β-strand	515-523	9	15
α-helix	525-530	6
β-strand	534-539	6	16
β-strand	547-552	6	16
β-strand	561-569	9	17
β-strand	574-575	2	18

Chain N: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	138	1	1
β-strand	141	1	2
β-strand	148-150	3	2
β-strand	152-153	2	1
β-strand	160-161	2	1
α-helix	169-179	11
β-strand	186-190	5	2
β-strand	233-237	5	2
α-helix	240-242	3
β-strand	243-248	6	3
β-strand	255-261	7	3
β-strand	264-266	3	3
β-strand	267-268	2	4
α-helix	276-284	9
β-strand	290	1	5
α-helix	298-300	3
β-strand	308-310	3	4
β-strand	314	1	6
α-helix	322-324	3
β-strand	326	1	6
β-strand	342	1	3
β-strand	345	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD5 antigen-like	N	protein	328	Homo sapiens	O43866 (AlphaFold model)
Ig-like domain-containing protein	A, B, K, L	protein	361	Homo sapiens	P01871 (AlphaFold model)
Immunoglobulin J chain	J	protein	169	Homo sapiens	P01591 (AlphaFold model)

Sequence of entity 1 (N), FASTA

>8R84_1 CD5 antigen-like (chains N)
SPSGVRLVGGLHRCEGRVEVEQKGQWGTVCDDGWDIKDVAVLCRELGCGAASGTPSGILY
EPPAEKEQKVLIQSVSCTGTEDTLAQCEQEEVYDCSHDEDAGASCENPESSFSPVPEGVR
LADGPGHCKGRVEVKHQNQWYTVCQTGWSLRAAKVVCRQLGCGRAVLTQKRCNKHAYGRK
PIWLSQMSCSGREATLQDCPSGPWGKNTCNHDEDTWVECEDPFDLRLVGGDNLCSGRLEV
LHKGVWGSVCDDNWGEKEDQVVCKQLGCGKSLSPSFRDRKCYGPGVGRIWLDNVRCSGEE
QSLEQCQHRFWGFHDCTHQEDVAVICSG

Sequence of entity 2 (A, B, K, L), FASTA

>8R84_2 Ig-like domain-containing protein (chains A, B, K, L)
DYKDDDDKGSGSGIAELPPKVSVFVPPRDGFFGNPRKSKLICQATGFSPRQIQVSWLREG
KQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDWLSQSMFTCRVDHRGLTFQQNASS
MCVPDQDTAIRVFAIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTN
ISESHPNATFSAVGEASICEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGVALHRPDVY
LLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRY
FAHSILTVSEEEWNTGETYTCVVAHEALPNRVTERTVDKSTGKPTLYNVSLVMSDTAGTC
Y

Sequence of entity 3 (J), FASTA

>8R84_3 Immunoglobulin J chain (chains J)
MKNHLLFWGVLAVFIKAVHVKAQEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNI
RIIVPLNNRENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSAT
ETCYTYDRNKCYTAVVPLVYGGETKMVETALTPDACYPDEQKLISEEDL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Primary citation

Cryo-EM reveals structural basis for human AIM/CD5L recognition of polymeric immunoglobulin M. Chen, Q., Ishii, K., Mori, H. et al. Nat Commun (2024) 15:9387-9387. DOI 10.1038/s41467-024-53615-5 · PubMed

Other PDB entries of the same protein (UniProt O43866 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8WYR 3.39 Å, Cryo-EM structure of human CD5L bound to IgM-Fc/J
8WYS 3.41 Å, Local map of human CD5L bound to IgM-Fc/J
8R83 3.57 Å, pentameric IgMFc-AIM complex global refinement

Browse structure collections

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