8BPG: FcMR binding at subunit Fcu3 of IgM pentamer

FcMR binding at subunit Fcu3 of IgM pentamer. Determined by electron microscopy at 3.1 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,650
Mol. weight: 206.7 kDa
Ligands: NAG
Released: 12 Apr 2023

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

Secondary structure: helices and β-sheets

8BPG contains 42 α-helices and 114 β-strands across 6 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.

Chains A and B: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	20
β-strand	32-38	7	21
β-strand	46-48	3	22
β-strand	50	1	23
β-strand	59	1	23
β-strand	63	1	22
α-helix	70-72	3
β-strand	76-81	6	21
β-strand	86-92	7	21
β-strand	101	1	24
β-strand	104-106	3	22
β-strand	116	1	22
β-strand	117	1	20
β-strand	119	1	24

Chains C and F: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	14
α-helix	351-353	3
α-helix	354-360	7
β-strand	366-370	5	14
β-strand	379-383	5	15
α-helix	396-399	4
β-strand	400	1	16
β-strand	404	1	16
β-strand	407	1	14
β-strand	410	1	14
α-helix	415-419	5
β-strand	424-429	6	15
β-strand	437	1	15
β-strand	440-441	2	15
β-strand	450	1	17
β-strand	453-457	5	18
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-479	11	18
β-strand	480	1	17
β-strand	485-489	5	19
β-strand	494	1	19
α-helix	495-496	2
β-strand	500-502	3	18
β-strand	506-507	2	18
α-helix	508	1
β-strand	515-524	10	18
α-helix	525-529	5
β-strand	534-539	6	19
β-strand	548-552	5	19
α-helix	558-560	3
β-strand	567	1	13

Chains D and E: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	6
α-helix	351-353	3
α-helix	354-360	7
β-strand	364-365	2	7
β-strand	366-370	5	6
β-strand	380-384	5	8
β-strand	389	1	8
α-helix	391-393	3
β-strand	399-400	2	9
β-strand	404-405	2	9
β-strand	411-412	2	7
α-helix	415-420	6
β-strand	424-428	5	8
β-strand	437-441	5	8
β-strand	450	1	10
β-strand	453-457	5	11
α-helix	458-460	3
α-helix	463-465	3
β-strand	470-479	10	11
β-strand	480	1	10
β-strand	485-490	6	12
β-strand	493-494	2	12
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	11
β-strand	506-507	2	11
α-helix	508	1
β-strand	515-523	9	11
α-helix	525-529	5
β-strand	534-539	6	12
β-strand	549-552	4	12
β-strand	567	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fas apoptotic inhibitory molecule 3	A, B	protein	234	Homo sapiens	O60667 (AlphaFold model)
Immunoglobulin heavy constant mu	C, D, E, F	protein	348	Homo sapiens	P01871 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8BPG_1 Fas apoptotic inhibitory molecule 3 (chains A, B)
RILPEVKVEGELGGSVTIKCPLPEMHVRIYLCREMAGSGTCGTVVSTTNFIKAEYKGRVT
LKQYPRKNLFLVEVTQLTESDSGVYACGAGMNTDRGKTQKVTLNVHSEYEPSWEEQPMPE
TPKWFHLPYLFQMPAYASSSKFVTRVTTPAQRGKVPPVHHSSPTTQITHRPRVSRASSVA
GDKPRTFLPSTTASKISALEGLLKPQTPSYNHHTRLHRQRALDYGSQSGREGQG

Sequence of entity 2 (C, D, E, F), FASTA

>8BPG_2 Immunoglobulin heavy constant mu (chains C, D, E, F)
IAELPPKVSVFVPPRDGFFGNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQ
AEAKESGPTTYKVTSTLTIKESDWLGQSMFTCRVDHRGLTFQQNASSMCVPDQDTAIRVF
AIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNATFSAV
GEASICEDDWNSGERFTCTVTHTDLPSPLKQTISRPKGVALHRPDVYLLPPAREQLNLRE
SATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPGRYFAHSILTVSEEEW
NTGETYTCVVAHEALPNRVTERTVDKSTGKPTLYNVSLVMSDTAGTCY

Ligands and cofactors

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

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
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
8BPE 3.63 Å, 8:1 binding of FcMR on IgM pentameric core
7YTD 3.71 Å, Cryo-EM structure of four human FcmR bound to IgM-Fc/J

Browse structure collections

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