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- EMDB-40054: Cryo-EM structure of fish immunogloblin M-Fc -

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Basic information

Entry
Database: EMDB / ID: EMD-40054
TitleCryo-EM structure of fish immunogloblin M-Fc
Map data
Sample
  • Complex: rainbow trout (Oncorhynchus mykiss) immunoglobulin M Fc
    • Protein or peptide: Teleost immunoglobulin M protein
KeywordsImmunoglobulin M / IgM / immune system
Biological speciesOncorhynchus mykiss (rainbow trout)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsLyu M / Stadtmueller BM / Malyutin AG
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: Nat Commun / Year: 2023
Title: The structure of the teleost Immunoglobulin M core provides insights on polymeric antibody evolution, assembly, and function.
Authors: Mengfan Lyu / Andrey G Malyutin / Beth M Stadtmueller /
Abstract: Polymeric (p) immunoglobulins (Igs) serve broad functions during vertebrate immune responses. Typically, pIgs contain between two and six Ig monomers, each with two antigen binding fragments and one ...Polymeric (p) immunoglobulins (Igs) serve broad functions during vertebrate immune responses. Typically, pIgs contain between two and six Ig monomers, each with two antigen binding fragments and one fragment crystallization (Fc). In addition, many pIgs assemble with a joining-chain (JC); however, the number of monomers and potential to include JC vary with species and heavy chain class. Here, we report the cryo-electron microscopy structure of IgM from a teleost (t) species, which does not encode JC. The structure reveals four tIgM Fcs linked through eight C-terminal tailpieces (Tps), which adopt a single β-sandwich-like domain (Tp assembly) located between two Fcs. Specifically, two of eight heavy chains fold uniquely, resulting in a structure distinct from mammalian IgM, which typically contains five IgM monomers, one JC and a centrally-located Tp assembly. Together with mutational analysis, structural data indicate that pIgs have evolved a range of assembly mechanisms and structures, each likely to support unique antibody effector functions.
History
DepositionMar 13, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40054.png

Downloads & links

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Map

FileDownload / File: emd_40054.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.855 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.34116507 - 0.6369556
Average (Standard dev.)0.00032436562 (±0.01303736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 300.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_40054_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40054_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : rainbow trout (Oncorhynchus mykiss) immunoglobulin M Fc

EntireName: rainbow trout (Oncorhynchus mykiss) immunoglobulin M Fc
Components
  • Complex: rainbow trout (Oncorhynchus mykiss) immunoglobulin M Fc
    • Protein or peptide: Teleost immunoglobulin M protein

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Supramolecule #1: rainbow trout (Oncorhynchus mykiss) immunoglobulin M Fc

SupramoleculeName: rainbow trout (Oncorhynchus mykiss) immunoglobulin M Fc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Heavy chain constant domains 3 and 4 including C-terminal tailpiece
Source (natural)Organism: Oncorhynchus mykiss (rainbow trout)

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Macromolecule #1: Teleost immunoglobulin M protein

MacromoleculeName: Teleost immunoglobulin M protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Oncorhynchus mykiss (rainbow trout)
Molecular weightTheoretical: 26.998514 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHHGHL VVITIIEPSL EDMLMNKKAQ LVCDVNELVP GFLSVKWEND NGKTLTSRKG VTDKIAILDI TYEDWSNGTV FYCAVDHME NLGDLVKKAY KRETGGVPQR PSVFLLAPAE QTSDNTVTLT CYVKDFYPKD VLVAWLVDDE PVERTSSSAL Y QFNTTSQI ...String:
HHHHHHHGHL VVITIIEPSL EDMLMNKKAQ LVCDVNELVP GFLSVKWEND NGKTLTSRKG VTDKIAILDI TYEDWSNGTV FYCAVDHME NLGDLVKKAY KRETGGVPQR PSVFLLAPAE QTSDNTVTLT CYVKDFYPKD VLVAWLVDDE PVERTSSSAL Y QFNTTSQI QSGRTYSVYS QLTFSNDLWK NEEVVYSCVV YHESMIKSTN IIMRTIDRTS NQPNLVNLSL NVPQRCMAQ

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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

Concentration0.1 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris-HClTris
150.0 mMNaClSodium chlorideSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.029 kPa / Details: Pelco easiGlow at 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3618 / Average electron dose: 60.0 e/Å2
Details: Images were collected with SerialEM using beam image-shift in a 3x3x3 pattern. A total of ~60 e/A2 was fractionated into 40 frames movies.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1300000
Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 61000
FSC plot (resolution estimation)

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