7YTD: Four human FcmR

Cryo-EM structure of four human FcmR bound to IgM-Fc/J. Determined by electron microscopy at 3.71 Å resolution. Released 1 Feb 2023.

Method: Electron microscopy
Resolution: 3.71 Å
Organism: Homo sapiens
Chains: 15
Atoms: 21,693
Mol. weight: 319.08 kDa
Ligands: NAG
Released: 1 Feb 2023

Explore 7YTD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YTD contains 83 α-helices and 253 β-strands across 15 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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	346-347	2	1
β-strand	350	1	1
α-helix	351-353	3
α-helix	354-359	6
β-strand	364-372	9	1
β-strand	379-383	5	2
β-strand	389	1	2
β-strand	405-412	8	1
α-helix	415-419	5
β-strand	424-430	7	2
β-strand	433-441	9	2
β-strand	453-457	5	3
α-helix	458-460	3
α-helix	462-465	4
β-strand	470-477	8	3
β-strand	486-490	5	4
β-strand	493-494	2	4
β-strand	501-502	2	3
β-strand	506-507	2	3
β-strand	515-523	9	3
α-helix	525-529	5
β-strand	534-539	6	4
β-strand	547-552	6	4
β-strand	561	1	5
β-strand	565	1	6
β-strand	568-569	2	7

Chain B: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	8
α-helix	351-353	3
α-helix	354-360	7
β-strand	363-365	3	9
β-strand	366-370	5	8
β-strand	381-383	3	10
β-strand	411-413	3	9
α-helix	416-420	5
β-strand	423-424	2	11
β-strand	425-428	4	10
β-strand	437-438	2	10
β-strand	441-442	2	11
β-strand	453-457	5	12
α-helix	458-460	3
α-helix	463-466	4
β-strand	470-479	10	12
β-strand	485-490	6	13
β-strand	493-494	2	13
α-helix	495-496	2
β-strand	500-502	3	12
α-helix	503-505	3
β-strand	506-507	2	12
β-strand	515-523	9	12
α-helix	525-529	5
β-strand	534-539	6	13
β-strand	547-552	6	13
β-strand	561	1	5
β-strand	567	1	14

Chain C: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	15
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-372	9	15
β-strand	380-383	4	16
β-strand	389	1	16
α-helix	391-393	3
α-helix	396-398	3
β-strand	399-400	2	15
β-strand	404-407	4	15
β-strand	410-412	3	15
α-helix	415-419	5
β-strand	424-428	5	16
β-strand	437-441	5	16
β-strand	450	1	17
β-strand	453-457	5	18
α-helix	458-460	3
β-strand	470-479	10	18
β-strand	480	1	17
β-strand	485-490	6	19
β-strand	493-494	2	19
β-strand	500-502	3	18
β-strand	506-507	2	18
β-strand	508	1	20
β-strand	511	1	20
β-strand	515-517	3	18
β-strand	519-523	5	18
α-helix	525-529	5
β-strand	534-539	6	19
β-strand	547-552	6	19
β-strand	561	1	5
β-strand	567	1	14

Chain D: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	21
α-helix	351-353	3
α-helix	354-359	6
β-strand	365-370	6	21
β-strand	379-383	5	22
β-strand	389	1	22
α-helix	398-400	3
β-strand	406-411	6	21
α-helix	415-418	4
β-strand	424	1	23
β-strand	425-429	5	22
β-strand	437-438	2	22
β-strand	441	1	23
β-strand	453-457	5	24
α-helix	458-460	3
α-helix	461-466	6
β-strand	469	1	25
β-strand	472-479	8	24
β-strand	485-490	6	26
β-strand	493-494	2	26
β-strand	500-502	3	24
α-helix	503-505	3
β-strand	506-507	2	24
β-strand	515-521	7	24
β-strand	524	1	25
α-helix	525-530	6
β-strand	535-539	5	26
β-strand	548-550	3	26
α-helix	558-560	3
β-strand	562	1	27

Chain E: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	28
α-helix	354-359	6
β-strand	365-373	9	28
β-strand	379-383	5	29
α-helix	391-393	3
β-strand	400	1	28
β-strand	404-411	8	28
α-helix	415-418	4
β-strand	424-429	6	29
β-strand	437-441	5	29
β-strand	450	1	30
β-strand	453-457	5	31
α-helix	458-460	3
α-helix	463-466	4
β-strand	470-479	10	31
β-strand	480	1	30
β-strand	485-489	5	32
β-strand	490	1	33
β-strand	493	1	33
β-strand	500-502	3	31
β-strand	506-507	2	31
β-strand	515-523	9	31
α-helix	525-528	4
β-strand	534-539	6	32
β-strand	548-552	5	32
β-strand	562	1	27

Chain F: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	34
α-helix	354-360	7
β-strand	365	1	35
β-strand	366-369	4	34
β-strand	373	1	36
β-strand	379-383	5	37
α-helix	398-400	3
β-strand	404	1	36
β-strand	411	1	35
α-helix	415-418	4
β-strand	424-429	6	37
α-helix	436	1
β-strand	437	1	37
β-strand	440-441	2	37
β-strand	455-457	3	38
α-helix	458-460	3
α-helix	463-466	4
β-strand	470-479	10	38
β-strand	485-490	6	39
β-strand	493-494	2	39
α-helix	495-496	2
β-strand	501-502	2	38
α-helix	503-505	3
β-strand	506-507	2	38
β-strand	515-523	9	38
α-helix	525-530	6
β-strand	535-539	5	39
β-strand	547-550	4	39
β-strand	565-567	3	40

Chain G: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	41
α-helix	354-358	5
β-strand	364-372	9	41
β-strand	379-383	5	42
β-strand	394	1	41
β-strand	405-412	8	41
α-helix	415-420	6
α-helix	422-423	2
β-strand	424-429	6	42
β-strand	437-441	5	42
β-strand	450	1	43
β-strand	453-457	5	44
α-helix	458-460	3
α-helix	463-465	3
β-strand	470-479	10	44
β-strand	480	1	43
β-strand	485-490	6	45
β-strand	493-494	2	45
α-helix	495-496	2
β-strand	500-502	3	44
β-strand	506-507	2	44
β-strand	515-523	9	44
α-helix	525-530	6
β-strand	535-539	5	45
β-strand	547-550	4	45
α-helix	554-556	3
β-strand	565-567	3	40

Chain H: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	46
α-helix	354-360	7
β-strand	365-370	6	46
β-strand	379-383	5	47
α-helix	398-399	2
β-strand	400	1	48
β-strand	404	1	48
β-strand	409-411	3	46
α-helix	415-420	6
β-strand	424-429	6	47
β-strand	437-441	5	47
β-strand	455-457	3	49
α-helix	458-460	3
α-helix	463-465	3
β-strand	470-475	6	49
β-strand	479	1	50
β-strand	486-490	5	51
β-strand	493-494	2	51
α-helix	495-496	2
β-strand	500-502	3	49
β-strand	506-507	2	50
β-strand	515-516	2	50
β-strand	519-523	5	49
α-helix	525-529	5
β-strand	535-539	5	51
β-strand	547-550	4	51
β-strand	566	1	40

7 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
Immunoglobulin heavy constant mu	A, B, C, D, E, F, G, H, K, L	protein	231	Homo sapiens	P01871 (AlphaFold model)
Immunoglobulin J chain	J	protein	136	Homo sapiens	P01591 (AlphaFold model)
Fas apoptotic inhibitory molecule 3	R, S, U, V	protein	107	Homo sapiens	O60667 (AlphaFold model)

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

>7YTD_1 Immunoglobulin heavy constant mu (chains A, B, C, D, E, F, G, H, K, L)
IRVFAIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNAT
FSAVGEASICEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGVALHRPDVYLLPPAREQL
NLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRYFAHSILTVS
EEEWNTGETYTCVVAHEALPNRVTERTVDKSTGKPTLYNVSLVMSDTAGTC

Sequence of entity 2 (J), FASTA

>7YTD_2 Immunoglobulin J chain (chains J)
EDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNRENISDPTSPLRTRF
VYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLVYGGE
TKMVETALTPDACYPD

Sequence of entity 3 (R, S, U, V), FASTA

>7YTD_3 Fas apoptotic inhibitory molecule 3 (chains R, S, U, V)
RILPEVKVEGELGGSVTIKCPLPEMHVRIYLCREMAGSGTCGTVVSTTNFIKAEYKGRVT
LKQYPRKNLFLVEVTQLTESDSGVYACGAGMNTDRGKTQKVTLNVHS

Ligands and cofactors

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

Primary citation

Immunoglobulin M perception by Fc mu R. Li, Y., Shen, H., Zhang, R. et al. Nature (2023) 615:907-912. DOI 10.1038/s41586-023-05835-w · 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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