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- EMDB-13922: Cryo-EM structure of human monomeric IgM-Fc -

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Basic information

Entry
Database: EMDB / ID: EMD-13922
TitleCryo-EM structure of human monomeric IgM-Fc
Map data
Sample
  • Complex: human monomeric IgM-Fc
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
Keywordshuman monomeric IgM-Fc / IMMUNE SYSTEM
Function / homologyIsoform 2 of Immunoglobulin heavy constant mu
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen Q / Rosenthal P / Tolar P
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Cancer Research UKFC001143 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001143 United Kingdom
Wellcome TrustFC001143 United Kingdom
Cancer Research UKFC001185 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001185 United Kingdom
Wellcome TrustFC001185 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Cryomicroscopy reveals the structural basis for a flexible hinge motion in the immunoglobulin M pentamer.
Authors: Qu Chen / Rajesh Menon / Lesley J Calder / Pavel Tolar / Peter B Rosenthal /
Abstract: Immunoglobulin M (IgM) is the most ancient of the five isotypes of immunoglobulin (Ig) molecules and serves as the first line of defence against pathogens. Here, we use cryo-EM to image the structure ...Immunoglobulin M (IgM) is the most ancient of the five isotypes of immunoglobulin (Ig) molecules and serves as the first line of defence against pathogens. Here, we use cryo-EM to image the structure of the human full-length IgM pentamer, revealing antigen binding domains flexibly attached to the asymmetric and rigid core formed by the Cμ4 and Cμ3 constant regions and the J-chain. A hinge is located at the Cμ3/Cμ2 domain interface, allowing Fabs and Cμ2 to pivot as a unit both in-plane and out-of-plane. This motion is different from that observed in IgG and IgA, where the two Fab arms are able to swing independently. A biased orientation of one pair of Fab arms results from asymmetry in the constant domain (Cμ3) at the IgM subunit interacting most extensively with the J-chain. This may influence the multi-valent binding to surface-associated antigens and complement pathway activation. By comparison, the structure of the Fc fragment in the IgM monomer is similar to that of the pentamer, but is more dynamic in the Cμ4 domain.
History
DepositionNov 27, 2021-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13922.png

Downloads & links

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Map

FileDownload / File: emd_13922.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.784 Å		0.84 Å/pix.
x 256 pix.
= 214.784 Å		0.84 Å/pix.
x 256 pix.
= 214.784 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-4.5383687 - 6.066068
Average (Standard dev.)0.0044933027 (±0.0958546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13922_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13922_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13922_half_map_2.map
Projections & Slices
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Sample components

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Entire : human monomeric IgM-Fc

EntireName: human monomeric IgM-Fc
Components
  • Complex: human monomeric IgM-Fc
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu

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Supramolecule #1: human monomeric IgM-Fc

SupramoleculeName: human monomeric IgM-Fc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of Immunoglobulin heavy constant mu

MacromoleculeName: Isoform 2 of Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.687059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GVIAELPPKV SVFVPPRDGF FGNPRKSKLI CQATGFSPRQ IQVSWLREGK QVGSGVTTD QVQAEAKESG PTTYKVTSTL TIKESDWLSQ SMFTCRVDHR GLTFQQNASS MCVPDQDTAI RVFAIPPSFA S IFLTKSTK ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GVIAELPPKV SVFVPPRDGF FGNPRKSKLI CQATGFSPRQ IQVSWLREGK QVGSGVTTD QVQAEAKESG PTTYKVTSTL TIKESDWLSQ SMFTCRVDHR GLTFQQNASS MCVPDQDTAI RVFAIPPSFA S IFLTKSTK LTCLVTDLTT YDSVTISWTR QNGEAVKTHT NISESHPNAT FSAVGEASIS EDDWNSGERF TCTVTHTDLP SP LKQTISR PKGVALHRPD VYLLPPAREQ LNLRESATIT CLVTGFSPAD VFVQWMQRGQ PLSPEKYVTS APMPEPQAPG RYF AHSILT VSEEEWNTGE TYTCVVAHEA LPNRVTERTV DKSTEGEVSA DEEGFENEIA QLEYEISQLE QEIQALESGG GSGG GSENL YFQGGGSWSH PQFEKGGGSG GGSGGSAWSH PQFEK

UniProtKB: Isoform 2 of Immunoglobulin heavy constant mu

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 59595 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kxs

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 961072
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7qdo:
Cryo-EM structure of human monomeric IgM-Fc

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