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- PDB-9p6u: Cryo-EM structure of chimeric immunoglobulin M comprising bony fi... -

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Basic information

Entry
Database: PDB / ID: 9p6u
TitleCryo-EM structure of chimeric immunoglobulin M comprising bony fish and human sequences, hFcm-tFcm-chi3
ComponentsChimeric Immunoglobulin heavy constant mu
KeywordsIMMUNE SYSTEM / immunoglobulin M / fragment crystallization
Function / homology
Function and homology information


hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / IgM immunoglobulin complex / pre-B cell allelic exclusion / CD22 mediated BCR regulation / antigen binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Cell surface interactions at the vascular wall / B cell receptor signaling pathway ...hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / IgM immunoglobulin complex / pre-B cell allelic exclusion / CD22 mediated BCR regulation / antigen binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / antibacterial humoral response / blood microparticle / Potential therapeutics for SARS / defense response to Gram-negative bacterium / adaptive immune response / innate immune response / cell surface / : / extracellular exosome / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant mu
Similarity search - Component
Biological speciesHomo sapiens (human)
Oncorhynchus mykiss (rainbow trout)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLyu, M. / Stadtmueller, B.M.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimeric Immunoglobulin heavy constant mu
B: Chimeric Immunoglobulin heavy constant mu
C: Chimeric Immunoglobulin heavy constant mu
D: Chimeric Immunoglobulin heavy constant mu
E: Chimeric Immunoglobulin heavy constant mu
F: Chimeric Immunoglobulin heavy constant mu
G: Chimeric Immunoglobulin heavy constant mu
H: Chimeric Immunoglobulin heavy constant mu
K: Chimeric Immunoglobulin heavy constant mu
L: Chimeric Immunoglobulin heavy constant mu


Theoretical massNumber of molelcules
Total (without water)268,04010
Polymers268,04010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Chimeric Immunoglobulin heavy constant mu / Ig mu chain C region / Ig mu chain C region BOT / Ig mu chain C region GAL / Ig mu chain C region OU


Mass: 26804.037 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: His-tagged chimeric IgM comprising Oncorhynchus mykiss and human sequences, hFcm-tFcm-chi3
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Oncorhynchus mykiss (rainbow trout)
Gene: IGHM / Plasmid: pD2610-v1 / Cell (production host): embryo / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Tissue (production host): Kidney / References: UniProt: P01871
Has protein modificationY
Sequence detailsResidues 343-552 are from human (Homo Sapiens) and residues 553-575 are from rainbow trout ...Residues 343-552 are from human (Homo Sapiens) and residues 553-575 are from rainbow trout (Oncorhynchus mykiss).

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: pentameric chimeric immunoglobulin M-Fc comprising Oncorhynchus mykiss and human sequences
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.27 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Oncorhynchus mykiss (rainbow trout)8022
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK-293 / Plasmid: pD2610-v1
Buffer solutionpH: 7.8
Details: 1x tris buffered saline (20mM Tris-HCl and 150mL NaCl, pH 7.8)
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HClC4H11NO31
2150 mMsodium chlorideNaCl1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
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 imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 57.35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4012
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.

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 821548
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 244125 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 123.08 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004117220
ELECTRON MICROSCOPYf_angle_d0.805423600
ELECTRON MICROSCOPYf_chiral_restr0.04932750
ELECTRON MICROSCOPYf_plane_restr0.00673060
ELECTRON MICROSCOPYf_dihedral_angle_d14.42966260

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