8BPF: FcMR binding at subunit Fcu1 of IgM pentamer

FcMR binding at subunit Fcu1 of IgM pentamer. Determined by electron microscopy at 3.5 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 12
Atoms: 18,593
Mol. weight: 430.21 kDa
Ligands: NAG
Released: 12 Apr 2023

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

Secondary structure: helices and β-sheets

8BPF contains 86 α-helices and 230 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: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	1
α-helix	351-353	3
α-helix	354-360	7
β-strand	366-369	4	1
β-strand	380-384	5	2
β-strand	389	1	2
α-helix	391-393	3
α-helix	396-399	4
β-strand	400	1	3
β-strand	404	1	3
α-helix	415-419	5
β-strand	424-428	5	2
β-strand	437-440	4	2
β-strand	450	1	4
β-strand	453-457	5	5
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-479	11	5
β-strand	480	1	4
β-strand	485-490	6	6
β-strand	493-494	2	6
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	5
β-strand	506-507	2	5
β-strand	515-517	3	5
β-strand	519-524	6	5
α-helix	525-528	4
β-strand	534-539	6	6
β-strand	547-548	2	6
β-strand	551-552	2	6
β-strand	561-563	3	7
β-strand	565-569	5	8

Chain B: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	347	1	9
β-strand	350	1	10
α-helix	351-353	3
α-helix	354-360	7
β-strand	366	1	10
β-strand	369	1	9
β-strand	379-383	5	11
α-helix	391-393	3
α-helix	396-398	3
β-strand	400	1	12
β-strand	404	1	12
α-helix	415-420	6
β-strand	424-429	6	11
β-strand	440-441	2	11
β-strand	450	1	13
α-helix	451-452	2
β-strand	453-457	5	14
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-477	9	14
β-strand	480	1	13
β-strand	485-490	6	15
β-strand	493-494	2	15
α-helix	495-496	2
β-strand	500-502	3	14
α-helix	503-505	3
β-strand	506-507	2	14
β-strand	515-524	10	14
α-helix	525-530	6
β-strand	534-539	6	15
β-strand	548-552	5	15
β-strand	561-563	3	7

Chain C: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	16
α-helix	354-360	7
β-strand	364-372	9	16
β-strand	379-383	5	17
β-strand	389	1	17
α-helix	391-393	3
β-strand	405-412	8	16
α-helix	415-419	5
β-strand	424-430	7	17
β-strand	433-441	9	17
α-helix	447-449	3
β-strand	450	1	18
β-strand	455-457	3	19
α-helix	458-460	3
α-helix	461-464	4
β-strand	470-475	6	19
β-strand	476-479	4	20
β-strand	480	1	18
β-strand	485-490	6	21
β-strand	493-494	2	21
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	19
β-strand	506-507	2	20
β-strand	515-517	3	20
β-strand	519-523	5	19
α-helix	525-528	4
β-strand	535-539	5	21
β-strand	548-551	4	21
β-strand	561	1	7
β-strand	562	1	22

Chain D: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	23
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-370	7	23
β-strand	379-383	5	24
α-helix	396-398	3
β-strand	400	1	25
β-strand	404	1	25
β-strand	408-412	5	23
α-helix	415-420	6
β-strand	424	1	26
β-strand	425-429	5	24
α-helix	436	1
β-strand	437	1	24
β-strand	441	1	26
β-strand	450	1	27
β-strand	453-457	5	28
α-helix	458-460	3
α-helix	461-465	5
β-strand	470-477	8	28
β-strand	480	1	27
β-strand	485-490	6	29
β-strand	493-494	2	29
β-strand	500-501	2	28
β-strand	506-507	2	28
α-helix	508	1
β-strand	515-523	9	28
α-helix	525-530	6
β-strand	535-539	5	29
β-strand	547-551	5	29
β-strand	562	1	22
β-strand	565-567	3	30

Chain E: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	31
α-helix	351-353	3
α-helix	354-360	7
β-strand	366-372	7	31
β-strand	379-383	5	32
α-helix	391-393	3
β-strand	400	1	33
β-strand	404	1	33
β-strand	405-410	6	31
α-helix	415-420	6
β-strand	424	1	34
β-strand	425-429	5	32
β-strand	441	1	34
β-strand	453-457	5	35
α-helix	458-460	3
α-helix	462-465	4
β-strand	470-477	8	35
β-strand	485-490	6	36
β-strand	493-494	2	36
β-strand	500-502	3	35
β-strand	506	1	35
β-strand	516-523	8	35
α-helix	525-530	6
β-strand	534-539	6	36
β-strand	547-552	6	36
α-helix	554-556	3
β-strand	562	1	22
β-strand	565-567	3	30

Chain F: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	37
α-helix	354-360	7
β-strand	366-370	5	37
β-strand	380-383	4	38
β-strand	389	1	38
α-helix	392-393	2
α-helix	398-400	3
α-helix	415-420	6
β-strand	424-428	5	38
β-strand	437	1	38
β-strand	440-441	2	38
α-helix	450-452	3
β-strand	453-457	5	39
α-helix	458-460	3
α-helix	463-466	4
β-strand	470-479	10	39
β-strand	487-490	4	40
β-strand	493-494	2	40
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	39
β-strand	506-507	2	39
β-strand	515-523	9	39
α-helix	525-528	4
β-strand	535-538	4	40
β-strand	548-551	4	40
α-helix	554-557	4
β-strand	566-567	2	41

Chain G: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	42
α-helix	354-360	7
β-strand	364-365	2	43
β-strand	366-369	4	42
β-strand	379-381	3	44
β-strand	399-400	2	45
β-strand	404-405	2	45
β-strand	407	1	42
β-strand	411-412	2	43
α-helix	415-420	6
β-strand	424	1	46
β-strand	427-429	3	44
β-strand	441	1	46
β-strand	450	1	47
β-strand	453-457	5	48
α-helix	458-460	3
β-strand	469-471	3	49
β-strand	473-479	7	48
β-strand	480	1	47
β-strand	485-491	7	50
β-strand	493-494	2	50
β-strand	502	1	48
β-strand	506-507	2	48
α-helix	508	1
β-strand	515-519	5	48
β-strand	522-524	3	49
α-helix	525-528	4
β-strand	535-539	5	50
β-strand	548-550	3	50
β-strand	562	1	51
β-strand	566-567	2	41

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	52
α-helix	354-359	6
β-strand	365	1	53
β-strand	366-372	7	52
β-strand	379-383	5	54
α-helix	391-393	3
α-helix	396-399	4
β-strand	400	1	55
β-strand	404	1	55
β-strand	405-408	4	52
β-strand	411	1	53
α-helix	415-418	4
β-strand	424-429	6	54
α-helix	436	1
β-strand	437-441	5	54
β-strand	450	1	56
β-strand	453-457	5	57
α-helix	458-460	3
β-strand	470-479	10	57
β-strand	480	1	56
β-strand	485-490	6	58
β-strand	493-494	2	58
α-helix	495-496	2
β-strand	501-502	2	57
β-strand	515-517	3	57
β-strand	519-523	5	57
α-helix	525-528	4
β-strand	535-539	5	58
β-strand	547-550	4	58
β-strand	562-564	3	51
β-strand	567	1	41

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
Immunoglobulin heavy constant mu	A, B, C, D, E, F, G, H, K, L	protein	348	Homo sapiens	P01871 (AlphaFold model)
Fas apoptotic inhibitory molecule 3	I	protein	234	Homo sapiens	O60667 (AlphaFold model)
Immunoglobulin J chain	J	protein	159	Homo sapiens	P01591 (AlphaFold model)

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

>8BPF_1 Immunoglobulin heavy constant mu (chains A, B, C, D, E, F, G, H, K, L)
IAELPPKVSVFVPPRDGFFGNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQ
AEAKESGPTTYKVTSTLTIKESDWLGQSMFTCRVDHRGLTFQQNASSMCVPDQDTAIRVF
AIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNATFSAV
GEASICEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGVALHRPDVYLLPPAREQLNLRE
SATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRYFAHSILTVSEEEW
NTGETYTCVVAHEALPNRVTERTVDKSTGKPTLYNVSLVMSDTAGTCY

Sequence of entity 2 (I), FASTA

>8BPF_2 Fas apoptotic inhibitory molecule 3 (chains I)
RILPEVKVEGELGGSVTIKCPLPEMHVRIYLCREMAGSGTCGTVVSTTNFIKAEYKGRVT
LKQYPRKNLFLVEVTQLTESDSGVYACGAGMNTDRGKTQKVTLNVHSEYEPSWEEQPMPE
TPKWFHLPYLFQMPAYASSSKFVTRVTTPAQRGKVPPVHHSSPTTQITHRPRVSRASSVA
GDKPRTFLPSTTASKISALEGLLKPQTPSYNHHTRLHRQRALDYGSQSGREGQG

Sequence of entity 3 (J), FASTA

>8BPF_3 Immunoglobulin J chain (chains J)
MKNHLLFWGVLAVFIKAVHVKAQEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNI
RIIVPLNNRENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDNQIVTATQSNICDEDSAT
ETCYTYDRNKCYTAVVPLVYGGETKMVETALTPDACYPD

Ligands and cofactors

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

Primary citation

Structural basis for Fc receptor recognition of immunoglobulin M. Chen, Q., Menon, R.P., Masino, L. et al. Nat Struct Mol Biol (2023) 30:1033-1039. DOI 10.1038/s41594-023-00985-x · 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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