7YTE: Human FcmR-D1

crystal structure of human FcmR-D1 bound to IgM C4-domain. Determined by X-ray diffraction at 3.0 Å resolution. Released 1 Feb 2023.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,363
Mol. weight: 48.35 kDa
Released: 1 Feb 2023

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

Secondary structure: helices and β-sheets

7YTE contains 19 α-helices and 38 β-strands across 4 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, 11 β-strands

Element	Residues	Length	Sheet
α-helix	447-449	3
β-strand	450	1	1
β-strand	453-457	5	2
α-helix	458-460	3
α-helix	461-464	4
β-strand	469-479	11	2
β-strand	480	1	1
β-strand	485-490	6	3
β-strand	493-494	2	3
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	2
α-helix	503-505	3
β-strand	506-507	2	2
β-strand	515-524	10	2
α-helix	525-530	6
β-strand	534-539	6	3
β-strand	547-552	6	3

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	453-457	5	4
α-helix	458-460	3
α-helix	461-465	5
β-strand	469-479	11	4
β-strand	485-490	6	5
β-strand	493-494	2	5
α-helix	495-496	2
α-helix	497-499	3
β-strand	500-502	3	4
β-strand	506-507	2	4
β-strand	515-524	10	4
α-helix	525-529	5
β-strand	534-539	6	5
β-strand	547-552	6	5

Chain C: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	8
β-strand	33-38	6	9
β-strand	46-52	7	8
β-strand	57-63	7	8
β-strand	67-68	2	8
α-helix	70-72	3
β-strand	76-81	6	9
α-helix	82-84	3
β-strand	86-91	6	9
α-helix	96-98	3
β-strand	100-106	7	8
β-strand	116-123	8	8

Chain D: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
β-strand	22-28	7	6
β-strand	33-38	6	7
β-strand	46-52	7	6
β-strand	57-63	7	6
β-strand	67-68	2	6
α-helix	70-72	3
β-strand	76-81	6	7
α-helix	82-84	3
β-strand	86-91	6	7
α-helix	96-98	3
β-strand	100-106	7	6
β-strand	114-123	10	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ig mu chain C region secreted form	A, B	protein	112	Homo sapiens
Fas apoptotic inhibitory molecule 3	C, D	protein	107	Homo sapiens	O60667 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7YTE_1 Ig mu chain C region secreted form (chains A, B)
GVALHRPDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAP
MPEPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEALPNRVTERTVDKSTG

Sequence of entity 2 (C, D), FASTA

>7YTE_2 Fas apoptotic inhibitory molecule 3 (chains C, D)
RILPEVKVEGELGGSVTIKCPLPEMHVRIYLCREMAGSGTCGTVVSTTNFIKAEYKGRVT
LKQYPRKNLFLVEVTQLTESDSGVYACGAGMNTDRGKTQKVTLNVHS

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

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
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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