7YSG: Human FcmR

Cryo-EM structure of human FcmR bound to sIgM. Determined by electron microscopy at 3.18 Å resolution. Released 1 Feb 2023.

Method: Electron microscopy
Resolution: 3.18 Å
Organism: Homo sapiens
Chains: 16
Atoms: 25,676
Mol. weight: 380.71 kDa
Ligands: NAG
Released: 1 Feb 2023

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

Secondary structure: helices and β-sheets

7YSG contains 101 α-helices and 307 β-strands across 16 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: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	1
α-helix	351-353	3
α-helix	354-359	6
β-strand	363	1	2
β-strand	366-372	7	1
β-strand	381-383	3	3
β-strand	389-392	4	3
β-strand	397	1	1
β-strand	405-406	2	1
β-strand	413	1	2
α-helix	415-420	6
β-strand	424-427	4	3
β-strand	438-441	4	3
β-strand	453-457	5	4
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-477	9	4
β-strand	485-490	6	5
β-strand	516-524	9	4
α-helix	525-530	6
α-helix	532-533	2
β-strand	534-539	6	5
β-strand	545	1	5
β-strand	547-552	6	5
β-strand	561-563	3	6
β-strand	565-569	5	7

Chain B: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	346-349	4	8
α-helix	351-353	3
α-helix	354-359	6
β-strand	364-365	2	9
β-strand	367-370	4	8
β-strand	383	1	10
α-helix	396-399	4
β-strand	411-412	2	9
β-strand	425-428	4	10
β-strand	437-440	4	10
β-strand	453-457	5	11
α-helix	458-460	3
α-helix	461-464	4
β-strand	469-477	9	11
β-strand	485-489	5	12
β-strand	494	1	12
α-helix	495-496	2
β-strand	500-502	3	11
α-helix	503-505	3
β-strand	506-507	2	11
β-strand	515-524	10	11
α-helix	525-528	4
β-strand	534-539	6	12
β-strand	547-552	6	12
β-strand	561-563	3	6
β-strand	567	1	6

Chain C: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	13
α-helix	354-360	7
β-strand	363-372	10	13
β-strand	379-383	5	14
β-strand	389	1	14
α-helix	391-393	3
β-strand	399	1	13
β-strand	405-413	9	13
α-helix	415-420	6
β-strand	424-429	6	14
β-strand	437-441	5	14
β-strand	455-457	3	15
α-helix	458-460	3
α-helix	461-464	4
β-strand	471-475	5	15
β-strand	476-479	4	16
β-strand	485-490	6	17
β-strand	493-494	2	17
β-strand	500-502	3	15
α-helix	503-505	3
β-strand	506-507	2	16
β-strand	515-517	3	16
β-strand	519-522	4	15
α-helix	525-529	5
β-strand	535-539	5	17
β-strand	547-550	4	17
β-strand	561-562	2	6
β-strand	567	1	6

Chain D: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	18
α-helix	351-353	3
α-helix	354-360	7
β-strand	363-365	3	19
β-strand	366-369	4	18
β-strand	378-379	2	20
β-strand	382-383	2	21
α-helix	388	1
β-strand	389	1	21
α-helix	390	1
α-helix	392-393	2
α-helix	396-400	5
β-strand	411-413	3	19
α-helix	415-420	6
β-strand	424-428	5	21
β-strand	429-430	2	20
β-strand	437-441	5	21
β-strand	450	1	22
β-strand	453-457	5	23
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-479	10	23
β-strand	480	1	22
β-strand	485-490	6	24
β-strand	493-494	2	24
β-strand	500-502	3	23
α-helix	503-505	3
β-strand	506-507	2	23
β-strand	515-523	9	23
α-helix	525-529	5
β-strand	534-539	6	24
β-strand	547-552	6	24
β-strand	562-567	6	6

Chain E: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	25
α-helix	351-353	3
α-helix	354-359	6
β-strand	364-365	2	26
β-strand	366-370	5	25
β-strand	393	1	27
α-helix	405-407	3
β-strand	408	1	25
β-strand	409	1	27
β-strand	411-412	2	26
α-helix	415-420	6
β-strand	424-428	5	28
β-strand	437-441	5	28
β-strand	453-457	5	29
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-477	8	29
β-strand	485	1	30
β-strand	488-489	2	31
β-strand	500-502	3	29
α-helix	503-505	3
β-strand	516-523	8	29
α-helix	525-530	6
β-strand	535-537	3	31
β-strand	539	1	30
β-strand	549-551	3	31
β-strand	562-567	6	6

Chain F: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	351-353	3
α-helix	354-360	7
β-strand	379	1	32
β-strand	382-384	3	33
β-strand	389	1	33
β-strand	415	1	34
β-strand	419	1	34
β-strand	424-428	5	33
β-strand	429	1	32
β-strand	437-441	5	33
β-strand	453-457	5	35
α-helix	458-460	3
α-helix	461-466	6
β-strand	471-479	9	35
β-strand	485-490	6	36
β-strand	493-494	2	36
α-helix	495-496	2
β-strand	500-502	3	35
α-helix	503-505	3
β-strand	515-522	8	35
α-helix	525-528	4
β-strand	535-539	5	36
β-strand	547-550	4	36
β-strand	562	1	37
β-strand	565	1	38

Chain G: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	39
α-helix	351-353	3
α-helix	354-360	7
β-strand	363-369	7	39
β-strand	372	1	40
β-strand	380-384	5	41
α-helix	388	1
β-strand	389	1	41
α-helix	390-391	2
β-strand	404	1	40
β-strand	410-413	4	39
α-helix	415-419	5
β-strand	424-428	5	41
β-strand	453-457	5	42
α-helix	458-460	3
α-helix	461-464	4
β-strand	470-472	3	43
β-strand	473-477	5	42
β-strand	485-490	6	44
β-strand	493-494	2	44
α-helix	495-496	2
β-strand	500	1	43
β-strand	506-507	2	45
β-strand	515-516	2	45
β-strand	517-518	2	42
β-strand	521-523	3	43
α-helix	525-529	5
β-strand	535-539	5	44
β-strand	547-551	5	44
β-strand	562	1	37
β-strand	565	1	38

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	347-348	2	46
α-helix	351-353	3
α-helix	354-360	7
β-strand	365	1	47
β-strand	368-369	2	46
β-strand	381-382	2	48
β-strand	383	1	49
β-strand	389	1	49
α-helix	396-399	4
β-strand	400	1	50
β-strand	404	1	50
β-strand	411	1	47
α-helix	415-420	6
β-strand	426-427	2	48
β-strand	453-457	5	51
α-helix	458-460	3
α-helix	461-466	6
β-strand	470-479	10	51
β-strand	485-490	6	52
β-strand	493-494	2	52
α-helix	495-496	2
β-strand	500-502	3	51
α-helix	503-505	3
β-strand	506-507	2	51
β-strand	515-517	3	51
β-strand	519-523	5	51
α-helix	525-529	5
β-strand	535-539	5	52
β-strand	548-551	4	52
β-strand	562	1	37
β-strand	565	1	53

8 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	232	Homo sapiens	P01871 (AlphaFold model)
Immunoglobulin J chain	J	protein	136	Homo sapiens	P01591 (AlphaFold model)
Secretory component	P	protein	541	Homo sapiens	P01833 (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

>7YSG_1 Immunoglobulin heavy constant mu (chains A, B, C, D, E, F, G, H, K, L)
IRVFAIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNAT
FSAVGEASICEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGVALHRPDVYLLPPAREQL
NLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRYFAHSILTVS
EEEWNTGETYTCVVAHEALPNRVTERTVDKSTGKPTLYNVSLVMSDTAGTCY

Sequence of entity 2 (J), FASTA

>7YSG_2 Immunoglobulin J chain (chains J)
EDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNRENISDPTSPLRTRF
VYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSATETCYTYDRNKCYTAVVPLVYGGE
TKMVETALTPDACYPD

Sequence of entity 3 (P), FASTA

>7YSG_3 Secretory component (chains P)
KSPIFGPEEVNSVEGNSVSITCYYPPTSVNRHTRKYWCRQGARGGCITLISSEGYVSSKY
AGRANLTNFPENGTFVVNIAQLSQDDSGRYKCGLGINSRGLSFDVSLEVSQGPGLLNDTK
VYTVDLGRTVTINCPFKTENAQKRKSLYKQIGLYPVLVIDSSGYVNPNYTGRIRLDIQGT
GQLLFSVVINQLRLSDAGQYLCQAGDDSNSNKKNADLQVLKPEPELVYEDLRGSVTFHCA
LGPEVANVAKFLCRQSSGENCDVVVNTLGKRAPAFEGRILLNPQDKDGSFSVVITGLRKE
DAGRYLCGAHSDGQLQEGSPIQAWQLFVNEESTIPRSPTVVKGVAGGSVAVLCPYNRKES
KSIKYWCLWEGAQNGRCPLLVDSEGWVKAQYEGRLSLLEEPGNGTFTVILNQLTSRDAGF
YWCLTNGDTLWRTTVEIKIIEGEPNLKVPGNVTAVLGETLKVPCHFPCKFSSYEKYWCKW
NNTGCQALPSQDEGPSKAFVNCDENSRLVSLTLNLVTRADEGWYWCGVKQGHFYGETAAV
Y

Sequence of entity 4 (R, S, U, V), FASTA

>7YSG_4 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
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
8WYR 3.39 Å, Cryo-EM structure of human CD5L bound to IgM-Fc/J

Browse structure collections

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