8R83: Pentameric IgMFc-AIM complex global refinement

pentameric IgMFc-AIM complex global refinement. Determined by electron microscopy at 3.57 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.57 Å
Organism: Homo sapiens
Chains: 12
Atoms: 20,415
Mol. weight: 454.39 kDa
Ligands: NAG, CA
Released: 6 Nov 2024

Explore 8R83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R83 contains 84 α-helices and 250 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: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	60
α-helix	354-360	7
β-strand	363-372	10	60
β-strand	379-383	5	61
β-strand	389-390	2	61
β-strand	393-399	7	60
β-strand	405-413	9	60
α-helix	415-419	5
β-strand	424-429	6	61
β-strand	437-441	5	61
β-strand	450	1	62
β-strand	453-457	5	63
α-helix	458-460	3
α-helix	461-464	4
β-strand	469-479	11	63
β-strand	480	1	62
β-strand	485-490	6	64
β-strand	493-494	2	64
α-helix	495-496	2
β-strand	500-502	3	63
β-strand	506-507	2	63
β-strand	515-524	10	63
α-helix	525-530	6
β-strand	534-539	6	64
β-strand	547-552	6	64
β-strand	561	1	12
β-strand	564-569	6	13

Chain B: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	346-347	2	7
α-helix	350-352	3
α-helix	354-360	7
β-strand	363-366	4	7
β-strand	369-372	4	7
α-helix	375-377	3
β-strand	380-383	4	8
β-strand	393-396	4	7
β-strand	405-413	9	7
α-helix	415-417	3
β-strand	424-428	5	8
β-strand	437-441	5	8
α-helix	443-445	3
β-strand	450	1	9
β-strand	453-457	5	10
α-helix	458-460	3
α-helix	461-465	5
β-strand	470-479	10	10
β-strand	480	1	9
β-strand	485-490	6	11
β-strand	493-494	2	11
β-strand	500-502	3	10
β-strand	506-507	2	10
β-strand	515-523	9	10
α-helix	525-530	6
β-strand	534-539	6	11
β-strand	547-552	6	11
β-strand	561	1	12
β-strand	564-569	6	13

Chain C: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	346-348	3	14
α-helix	350-353	4
α-helix	354-360	7
β-strand	364	1	15
β-strand	368-372	5	14
β-strand	379-383	5	16
β-strand	389-390	2	16
β-strand	393-399	7	14
β-strand	405-410	6	14
β-strand	412	1	15
α-helix	415-420	6
β-strand	424-429	6	16
β-strand	437-441	5	16
β-strand	450	1	17
α-helix	451-452	2
β-strand	453-457	5	18
α-helix	458-460	3
α-helix	461-464	4
β-strand	470-479	10	18
β-strand	480	1	17
β-strand	485-490	6	19
β-strand	493-494	2	19
α-helix	495-496	2
β-strand	500-502	3	18
β-strand	506-507	2	18
β-strand	515-523	9	18
α-helix	525-530	6
β-strand	534-539	6	19
β-strand	547-552	6	19
α-helix	558-560	3
β-strand	561	1	12
β-strand	562-566	5	13
β-strand	569	1	13

Chain D: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	20
α-helix	354-360	7
β-strand	363-372	10	20
β-strand	379-384	6	21
β-strand	389-390	2	21
β-strand	393-399	7	20
β-strand	405-413	9	20
α-helix	415-418	4
β-strand	424-429	6	21
β-strand	437	1	21
β-strand	440-441	2	21
β-strand	450	1	22
β-strand	453-457	5	23
α-helix	458-460	3
α-helix	461-466	6
β-strand	469-479	11	23
β-strand	480	1	22
β-strand	485-490	6	24
β-strand	493-494	2	24
β-strand	500-502	3	23
β-strand	506-507	2	23
β-strand	515-524	10	23
α-helix	525-530	6
β-strand	533-539	7	24
β-strand	548-553	6	24
β-strand	562-566	5	13

Chain E: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	346-348	3	50
α-helix	350-353	4
α-helix	354-360	7
β-strand	364-366	3	50
β-strand	368-372	5	50
β-strand	379-383	5	51
β-strand	393-400	8	50
β-strand	404-412	9	50
α-helix	415-420	6
β-strand	425-429	5	51
β-strand	437-439	3	51
β-strand	450	1	52
α-helix	451-452	2
β-strand	453-457	5	53
α-helix	458-460	3
α-helix	461-465	5
β-strand	470-479	10	53
β-strand	480	1	52
β-strand	485-490	6	54
β-strand	493-494	2	54
α-helix	495-496	2
β-strand	500-502	3	53
β-strand	506-507	2	53
β-strand	515-523	9	53
α-helix	525-528	4
β-strand	534-539	6	54
β-strand	548	1	54
β-strand	551-552	2	54
β-strand	565-566	2	13

Chain F: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	55
α-helix	351-353	3
α-helix	354-360	7
β-strand	363-372	10	55
β-strand	379-383	5	56
β-strand	392-396	5	55
β-strand	405-413	9	55
α-helix	416-420	5
β-strand	424-429	6	56
β-strand	437-441	5	56
β-strand	450	1	57
β-strand	453-457	5	58
α-helix	458-460	3
α-helix	461-466	6
β-strand	469-479	11	58
β-strand	480	1	57
β-strand	484-490	7	59
β-strand	493-494	2	59
α-helix	495-496	2
β-strand	500-502	3	58
α-helix	503-505	3
β-strand	506-507	2	58
β-strand	515-524	10	58
α-helix	525-530	6
β-strand	534-540	7	59
β-strand	548	1	59
β-strand	551-552	2	59
β-strand	565-567	3	30

Chain G: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	346-347	2	43
β-strand	350	1	44
α-helix	354-359	6
β-strand	364-365	2	45
β-strand	366	1	44
β-strand	369-372	4	43
β-strand	379-383	5	46
β-strand	389-390	2	46
β-strand	393-396	4	43
α-helix	398-400	3
β-strand	405-410	6	43
β-strand	411-412	2	45
α-helix	415-420	6
β-strand	424-429	6	46
β-strand	437-441	5	46
β-strand	450	1	47
β-strand	453-457	5	48
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-479	11	48
β-strand	480	1	47
β-strand	485-490	6	49
β-strand	493-494	2	49
α-helix	495-496	2
β-strand	500-502	3	48
α-helix	503-505	3
β-strand	506-507	2	48
β-strand	515-524	10	48
α-helix	525-530	6
β-strand	534-539	6	49
β-strand	547-548	2	49
β-strand	551-552	2	49
β-strand	562	1	30
β-strand	565-567	3	30

Chain H: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	39
α-helix	351-353	3
α-helix	354-356	3
β-strand	363-372	10	39
β-strand	379-383	5	40
β-strand	389-390	2	40
β-strand	393-396	4	39
β-strand	405-413	9	39
α-helix	415-419	5
β-strand	424-429	6	40
β-strand	437-441	5	40
α-helix	450-452	3
β-strand	453-457	5	41
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-479	10	41
β-strand	486-490	5	42
β-strand	493-494	2	42
α-helix	495-496	2
β-strand	500-502	3	41
β-strand	506-507	2	41
β-strand	515-523	9	41
α-helix	525-529	5
β-strand	534-538	5	42
β-strand	548-552	5	42
α-helix	558-560	3
β-strand	561-567	7	30

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
CD5 antigen-like	N	protein	328	Homo sapiens	O43866 (AlphaFold model)
Ig-like domain-containing protein	A, B, C, D, E, F, G, H, 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

>8R83_1 CD5 antigen-like (chains N)
SPSGVRLVGGLHRCEGRVEVEQKGQWGTVCDDGWDIKDVAVLCRELGCGAASGTPSGILY
EPPAEKEQKVLIQSVSCTGTEDTLAQCEQEEVYDCSHDEDAGASCENPESSFSPVPEGVR
LADGPGHCKGRVEVKHQNQWYTVCQTGWSLRAAKVVCRQLGCGRAVLTQKRCNKHAYGRK
PIWLSQMSCSGREATLQDCPSGPWGKNTCNHDEDTWVECEDPFDLRLVGGDNLCSGRLEV
LHKGVWGSVCDDNWGEKEDQVVCKQLGCGKSLSPSFRDRKCYGPGVGRIWLDNVRCSGEE
QSLEQCQHRFWGFHDCTHQEDVAVICSG

Sequence of entity 2 (A, B, C, D, E, F, G, H, K, L), FASTA

>8R83_2 Ig-like domain-containing protein (chains A, B, C, D, E, F, G, H, K, L)
DYKDDDDKGSGSGIAELPPKVSVFVPPRDGFFGNPRKSKLICQATGFSPRQIQVSWLREG
KQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDWLSQSMFTCRVDHRGLTFQQNASS
MCVPDQDTAIRVFAIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTN
ISESHPNATFSAVGEASICEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGVALHRPDVY
LLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRY
FAHSILTVSEEEWNTGETYTCVVAHEALPNRVTERTVDKSTGKPTLYNVSLVMSDTAGTC
Y

Sequence of entity 3 (J), FASTA

>8R83_3 Immunoglobulin J chain (chains J)
MKNHLLFWGVLAVFIKAVHVKAQEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNI
RIIVPLNNRENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSAT
ETCYTYDRNKCYTAVVPLVYGGETKMVETALTPDACYPDEQKLISEEDL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
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
8R84 3.6 Å, pentameric IgMFc-AIM complex focused refinement

Browse structure collections

About this viewer

MolViewer shows 8R83 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.