7QDO: Human monomeric IgM-Fc

Cryo-EM structure of human monomeric IgM-Fc. Determined by electron microscopy at 3.6 Å resolution. Released 26 Oct 2022.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,304
Mol. weight: 95.37 kDa
Released: 26 Oct 2022

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

Secondary structure: helices and β-sheets

7QDO contains 16 α-helices and 40 β-strands across 2 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: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	346-350	5	7
α-helix	351-353	3
α-helix	354-360	7
β-strand	363-370	8	7
β-strand	380-383	4	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	409-413	5	7
α-helix	415-420	6
β-strand	424	1	10
β-strand	425-428	4	8
β-strand	437-438	2	8
β-strand	441	1	10
α-helix	450-452	3
β-strand	453-457	5	11
α-helix	458-460	3
β-strand	470-479	10	11
β-strand	485-490	6	12
β-strand	493-494	2	12
α-helix	495-496	2
β-strand	500-502	3	11
β-strand	506-507	2	11
β-strand	515-523	9	11
α-helix	525-529	5
β-strand	534-539	6	12
β-strand	548-550	3	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Immunoglobulin heavy constant mu	A, B	protein	440	Homo sapiens	P01871 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7QDO_1 Isoform 2 of Immunoglobulin heavy constant mu (chains A, B)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGVIAELPPKVSVFVPPRDGFFGNPRKSKLI
CQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDWLSQS
MFTCRVDHRGLTFQQNASSMCVPDQDTAIRVFAIPPSFASIFLTKSTKLTCLVTDLTTYD
SVTISWTRQNGEAVKTHTNISESHPNATFSAVGEASISEDDWNSGERFTCTVTHTDLPSP
LKQTISRPKGVALHRPDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLS
PEKYVTSAPMPEPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEALPNRVTERTVDKST
EGEVSADEEGFENEIAQLEYEISQLEQEIQALESGGGSGGGSENLYFQGGGSWSHPQFEK
GGGSGGGSGGSAWSHPQFEK

Primary citation

Cryomicroscopy reveals the structural basis for a flexible hinge motion in the immunoglobulin M pentamer. Chen, Q., Menon, R., Calder, L.J. et al. Nat Commun (2022) 13:6314-6314. DOI 10.1038/s41467-022-34090-2 · 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

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