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- EMDB-71326: Cryo-EM structure of chimeric immunoglobulin M comprising bony fi... -

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Basic information

Entry
Database: EMDB / ID: EMD-71326
TitleCryo-EM structure of chimeric immunoglobulin M comprising bony fish and human sequences, hFcm-tFcm-chi3
Map data
Sample
  • Complex: pentameric chimeric immunoglobulin M-Fc comprising Oncorhynchus mykiss and human sequences
    • Protein or peptide: Chimeric Immunoglobulin heavy constant mu
Keywordsimmunoglobulin M / fragment crystallization / IMMUNE SYSTEM
Biological speciesHomo sapiens (human) / Oncorhynchus mykiss (rainbow trout)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLyu M / Stadtmueller BM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI165570 United States
CitationJournal: bioRxiv / Year: 2025
Title: Chimeric Immunoglobulin and human Immunoglobulin M structures provide insights on joining-chain independent assembly and function.
Authors: Mengfan Lyu / Beth M Stadtmueller /
Abstract: Polymeric (p) immunoglobulins (Igs) play critical roles in vertebrate immunity. IgM is the evolutionarily oldest pIg and functions both in circulation and in the mucosa. pIgM typically comprises ...Polymeric (p) immunoglobulins (Igs) play critical roles in vertebrate immunity. IgM is the evolutionarily oldest pIg and functions both in circulation and in the mucosa. pIgM typically comprises between four and six IgM monomers and up to one joining chain (JC), which in mammals facilitates pIg assembly and promotes delivery to mucosal secretions. Bony fish (teleosts) lack JC and assemble tetrameric IgM whereas humans can express JC-containing pentamers and JC-free hexamers. Here we report cryo-electron microscopy structures of two JC-free chimeric IgM, comprising bony fish and human sequences, and the structure of human hexameric IgM. Chimeric IgM structures adopted unique pentameric geometry distinct from both human and fish pIgM whereas the human hexameric IgM structure adopted hexagonal geometry similar to JC-containing pentameric IgM, albeit with structural differences in center of the molecule. Together results provide new insights on how IgM heavy chain motifs contribute to JC-free pIgM assembly and reveal plasticity of this process, which can be manipulated to create pIg structures not observed in nature. Moreover, we found that antigen-targeting chimeric IgM could neutralize toxin cytotoxicity, indicating potential to engineer uniquely structured pIgs to prevent or treat disease.
History
DepositionJun 20, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71326.png

Downloads & links

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Map

FileDownload / File: emd_71326.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 423.2 Å		1.06 Å/pix.
x 400 pix.
= 423.2 Å		1.06 Å/pix.
x 400 pix.
= 423.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.92559713 - 1.610976
Average (Standard dev.)0.00037103725 (±0.01818381)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71326_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_71326_half_map_2.map
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Sample components

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Entire : pentameric chimeric immunoglobulin M-Fc comprising Oncorhynchus m...

EntireName: pentameric chimeric immunoglobulin M-Fc comprising Oncorhynchus mykiss and human sequences
Components
  • Complex: pentameric chimeric immunoglobulin M-Fc comprising Oncorhynchus mykiss and human sequences
    • Protein or peptide: Chimeric Immunoglobulin heavy constant mu

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Supramolecule #1: pentameric chimeric immunoglobulin M-Fc comprising Oncorhynchus m...

SupramoleculeName: pentameric chimeric immunoglobulin M-Fc comprising Oncorhynchus mykiss and human sequences
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 270 KDa

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Macromolecule #1: Chimeric Immunoglobulin heavy constant mu

MacromoleculeName: Chimeric Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 1
Details: His-tagged chimeric IgM comprising Oncorhynchus mykiss and human sequences, hFcm-tFcm-chi3
Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Oncorhynchus mykiss (rainbow trout)
Molecular weightTheoretical: 26.804037 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHSGTA IRVFAIPPSF ASIFLTKSTK LTCLVTDLTT YDSVTISWTR QNGEAVKTHT NISESHPNAT FSAVGEASIC EDDWNSGER FTCTVTHTDL PSPLKQTISR PKGVALHRPD VYLLPPAREQ LNLRESATIT CLVTGFSPAD VFVQWMQRGQ P LSPEKYVT ...String:
HHHHHHSGTA IRVFAIPPSF ASIFLTKSTK LTCLVTDLTT YDSVTISWTR QNGEAVKTHT NISESHPNAT FSAVGEASIC EDDWNSGER FTCTVTHTDL PSPLKQTISR PKGVALHRPD VYLLPPAREQ LNLRESATIT CLVTGFSPAD VFVQWMQRGQ P LSPEKYVT SAPMPEPQAP GRYFAHSILT VSEEEWNTGE TYTCVVAHEA LPNRVTERTV DRTSNQPNLV NLSLNVPQRC MA Q

UniProtKB: 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: 7.8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris-HCl
150.0 mMNaClsodium chloride

Details: 1x tris buffered saline (20mM Tris-HCl and 150mL NaCl, pH 7.8)
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Cryo-EM grids were prepared at 4 degree celsius, 100% humidity, with blot force of 3, wait time of 2 seconds, and blotting time of 2 seconds in a Vitrobot Mark IV (Thermo Fisher)..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 4012 / Average electron dose: 57.35 e/Å2
Details: Movies were collected on Titan Krios G4 Cryo-TEM (Thermo Fisher) operating at 300kV. 1986 movies were recorded on untilted stage whereas 2026 movies were recored on 30 degree tilted stage. ...Details: Movies were collected on Titan Krios G4 Cryo-TEM (Thermo Fisher) operating at 300kV. 1986 movies were recorded on untilted stage whereas 2026 movies were recored on 30 degree tilted stage. All movies were recorded using SerialEM on a post-GIF K3 Direct Electron Detector (Gatan) with 57.35 e/A2 total dose.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 821548
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 244125
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9p6u:
Cryo-EM structure of chimeric immunoglobulin M comprising bony fish and human sequences, hFcm-tFcm-chi3

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