8BPE: 8:1 binding of FcMR on IgM pentameric core

8:1 binding of FcMR on IgM pentameric core. Determined by electron microscopy at 3.63 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 3.63 Å
Organism: Homo sapiens
Chains: 19
Atoms: 24,195
Mol. weight: 612.76 kDa
Ligands: NAG
Released: 12 Apr 2023

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

Secondary structure: helices and β-sheets

8BPE contains 101 α-helices and 321 β-strands across 19 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	94
α-helix	351-353	3
α-helix	354-359	6
β-strand	366-369	4	94
β-strand	380-384	5	95
β-strand	389	1	95
α-helix	391-393	3
α-helix	396-399	4
β-strand	400	1	96
β-strand	404	1	96
α-helix	415-419	5
β-strand	424-428	5	95
β-strand	437-440	4	95
β-strand	450	1	97
β-strand	453-457	5	98
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-479	11	98
β-strand	480	1	97
β-strand	485-490	6	99
β-strand	493-494	2	99
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	98
β-strand	506-507	2	98
β-strand	515-517	3	98
β-strand	519-524	6	98
α-helix	525-528	4
β-strand	534-539	6	99
β-strand	547-548	2	99
β-strand	551-552	2	99
β-strand	561-563	3	7
β-strand	565-569	5	100

Chain B: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	347	1	87
β-strand	350	1	88
α-helix	351-353	3
α-helix	354-360	7
β-strand	366	1	88
β-strand	369	1	87
β-strand	379-383	5	89
α-helix	391-393	3
α-helix	396-398	3
β-strand	400	1	90
β-strand	404	1	90
α-helix	415-420	6
β-strand	424-429	6	89
β-strand	440-441	2	89
β-strand	450	1	91
α-helix	451-452	2
β-strand	453-457	5	92
α-helix	458-460	3
α-helix	461-464	4
β-strand	469-479	11	92
β-strand	480	1	91
β-strand	485-490	6	93
β-strand	493-494	2	93
α-helix	495-496	2
β-strand	500-502	3	92
α-helix	503-505	3
β-strand	506-507	2	92
β-strand	515-524	10	92
α-helix	525-530	6
β-strand	534-539	6	93
β-strand	548-552	5	93
β-strand	561-563	3	7

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	1
α-helix	354-360	7
β-strand	364-372	9	1
β-strand	379-383	5	2
β-strand	405-412	8	1
α-helix	415-419	5
β-strand	424-430	7	2
β-strand	433-441	9	2
α-helix	447-449	3
β-strand	450	1	3
β-strand	455-457	3	4
α-helix	458-460	3
α-helix	461-464	4
β-strand	470-475	6	4
β-strand	476-479	4	5
β-strand	480	1	3
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	4
β-strand	506-507	2	5
β-strand	515-517	3	5
β-strand	519-523	5	4
α-helix	525-528	4
β-strand	535-539	5	6
β-strand	548-551	4	6
β-strand	561	1	7
β-strand	562	1	8

Chain D: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	30
α-helix	351-353	3
α-helix	354-360	7
β-strand	366-370	5	30
β-strand	379-383	5	31
α-helix	396-399	4
β-strand	400	1	32
β-strand	404	1	32
β-strand	407	1	30
β-strand	410	1	30
α-helix	415-419	5
β-strand	424-429	6	31
β-strand	437	1	31
β-strand	440-441	2	31
β-strand	450	1	33
β-strand	453-457	5	34
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-479	11	34
β-strand	480	1	33
β-strand	485-489	5	35
β-strand	494	1	35
α-helix	495-496	2
β-strand	500-502	3	34
β-strand	506-507	2	34
α-helix	508	1
β-strand	515-524	10	34
α-helix	525-529	5
β-strand	534-539	6	35
β-strand	548-552	5	35
α-helix	558-560	3
β-strand	562	1	8
β-strand	567	1	36

Chain E: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	55
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-365	2	56
β-strand	366-370	5	55
β-strand	380-384	5	57
β-strand	389	1	57
α-helix	391-393	3
β-strand	399-400	2	58
β-strand	404-405	2	58
β-strand	411-412	2	56
α-helix	415-420	6
β-strand	424-428	5	57
β-strand	437-441	5	57
β-strand	450	1	59
β-strand	453-457	5	60
α-helix	458-460	3
α-helix	463-465	3
β-strand	470-479	10	60
β-strand	480	1	59
β-strand	485-490	6	61
β-strand	493-494	2	61
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	60
β-strand	506-507	2	60
α-helix	508	1
β-strand	515-523	9	60
α-helix	525-529	5
β-strand	534-539	6	61
β-strand	549-552	4	61
β-strand	562	1	8
β-strand	567	1	36

Chain F: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	42
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-365	2	43
β-strand	366-370	5	42
β-strand	380-384	5	44
β-strand	389	1	44
α-helix	391-393	3
β-strand	399-400	2	45
β-strand	404-405	2	45
β-strand	411-412	2	43
α-helix	415-420	6
β-strand	424-428	5	44
β-strand	437-441	5	44
β-strand	450	1	46
β-strand	453-457	5	47
α-helix	458-460	3
α-helix	463-465	3
β-strand	470-479	10	47
β-strand	480	1	46
β-strand	485-490	6	48
β-strand	493-494	2	48
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	47
β-strand	506-507	2	47
α-helix	508	1
β-strand	515-523	9	47
α-helix	525-529	5
β-strand	534-539	6	48
β-strand	549-552	4	48
β-strand	565-567	3	16

Chain G: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	49
α-helix	351-353	3
α-helix	354-360	7
β-strand	366-370	5	49
β-strand	379-383	5	50
α-helix	396-399	4
β-strand	400	1	51
β-strand	404	1	51
β-strand	407	1	49
β-strand	410	1	49
α-helix	415-419	5
β-strand	424-429	6	50
β-strand	437	1	50
β-strand	440-441	2	50
β-strand	450	1	52
β-strand	453-457	5	53
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-479	11	53
β-strand	480	1	52
β-strand	485-489	5	54
β-strand	494	1	54
α-helix	495-496	2
β-strand	500-502	3	53
β-strand	506-507	2	53
α-helix	508	1
β-strand	515-524	10	53
α-helix	525-529	5
β-strand	534-539	6	54
β-strand	548-552	5	54
α-helix	558-560	3
β-strand	562	1	15
β-strand	565-567	3	16

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	347-350	4	9
α-helix	354-359	6
β-strand	365	1	10
β-strand	366-372	7	9
β-strand	379-383	5	11
α-helix	391-393	3
α-helix	396-399	4
β-strand	400	1	12
β-strand	404	1	12
β-strand	405-408	4	9
β-strand	411	1	10
α-helix	415-418	4
β-strand	424-429	6	11
α-helix	436	1
β-strand	437-441	5	11
α-helix	450-452	3
β-strand	453-457	5	13
α-helix	458-460	3
β-strand	470-479	10	13
β-strand	485-490	6	14
β-strand	493-494	2	14
α-helix	495-496	2
β-strand	501-502	2	13
β-strand	515-517	3	13
β-strand	519-523	5	13
α-helix	525-528	4
β-strand	535-539	5	14
β-strand	547-550	4	14
β-strand	562	1	15
β-strand	565	1	16
β-strand	567	1	17

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	348	Homo sapiens
Fas apoptotic inhibitory molecule 3	I, M, N, O, P, Q, R, S	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

>8BPE_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, M, N, O, P, Q, R, S), FASTA

>8BPE_2 Fas apoptotic inhibitory molecule 3 (chains I, M, N, O, P, Q, R, S)
RILPEVKVEGELGGSVTIKCPLPEMHVRIYLCREMAGSGTCGTVVSTTNFIKAEYKGRVT
LKQYPRKNLFLVEVTQLTESDSGVYACGAGMNTDRGKTQKVTLNVHSEYEPSWEEQPMPE
TPKWFHLPYLFQMPAYASSSKFVTRVTTPAQRGKVPPVHHSSPTTQITHRPRVSRASSVA
GDKPRTFLPSTTASKISALEGLLKPQTPSYNHHTRLHRQRALDYGSQSGREGQG

Sequence of entity 3 (J), FASTA

>8BPE_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	8

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 O60667 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7YTE 3.0 Å, crystal structure of human FcmR-D1 bound to IgM C4-domain
8BPG 3.1 Å, FcMR binding at subunit Fcu3 of IgM pentamer
7YSG 3.18 Å, Cryo-EM structure of human FcmR bound to sIgM
7YTC 3.39 Å, Cryo-EM structure of human FcmR bound to IgM-Fc/J
8BPF 3.5 Å, FcMR binding at subunit Fcu1 of IgM pentamer
7YTD 3.71 Å, Cryo-EM structure of four human FcmR bound to IgM-Fc/J

Browse structure collections

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