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- EMDB-71327: Cryo-EM structure of chimeric immunoglobulin M comprising bony fi... -

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Basic information

Entry
Database: EMDB / ID: EMD-71327
TitleCryo-EM structure of chimeric immunoglobulin M comprising bony fish and human sequences, hFcm-tFcm-chi4
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: 3.92 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_71327.png

Downloads & links

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Map

FileDownload / File: emd_71327.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-0.84772563 - 1.2904516
Average (Standard dev.)0.00046326296 (±0.017205833)
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: #1

Fileemd_71327_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_71327_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. Residues 343-546 are from human (Homo sapiens) and residues 547-575 are from rainbow trout (Oncorhynchus mykiss), hFcm-tFcm-chi4.
Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Oncorhynchus mykiss (rainbow trout)
Molecular weightTheoretical: 26.846229 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 LPNRIIMRTI 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 hydrochloride
150.0 mMNaClsodium chloride

Details: 20mM Tris-HCl, 150mM NaCl, pH7.8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3341 / Average electron dose: 57.35 e/Å2
Details: Movies were collected on Titan Krios G4 Cryo-TEM (Thermo Fisher) operating at 300kV. 1679 movies were recorded on untilted stage whereas 1662 movies were recored on 30 degree tilted stage. ...Details: Movies were collected on Titan Krios G4 Cryo-TEM (Thermo Fisher) operating at 300kV. 1679 movies were recorded on untilted stage whereas 1662 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: 3.0 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: 477625
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 244941
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient
Output model

PDB-9p6v:
Cryo-EM structure of chimeric immunoglobulin M comprising bony fish and human sequences, hFcm-tFcm-chi4

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