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- EMDB-77750: 1D6 Fab/NA25:Ab complex -

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Basic information

Entry
Database: EMDB / ID: EMD-77750
Title1D6 Fab/NA25:Ab complex
Map data
Sample
  • Complex: Complex of 1D6 Fab and NA25:Ab
KeywordsMHCII / Antibody / T-cell receptor / IMMUNE SYSTEM
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsDu J / Pallesen J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2026
Title: Generation and MHC class II loading of an endogenous influenza epitope revealed by a T cell receptor-like antibody.
Authors: Linlin Yang / Michael J Hogan / Stephen D Carro / Emma J Hedgepeth / Jianqiu Du / Mary E O'Mara / Kathleen S Krauss / Robert Novak / Christabel Ameyaw Baah / Nhu Le / Chaitali Bhadiadra / ...Authors: Linlin Yang / Michael J Hogan / Stephen D Carro / Emma J Hedgepeth / Jianqiu Du / Mary E O'Mara / Kathleen S Krauss / Robert Novak / Christabel Ameyaw Baah / Nhu Le / Chaitali Bhadiadra / Jesper Pallesen / Laurence C Eisenlohr /
Abstract: CD4 T cells coordinate immune responses to infections and cancers and initiate many autoimmune diseases, yet the intracellular pathways that generate the peptide antigens they recognize remain ...CD4 T cells coordinate immune responses to infections and cancers and initiate many autoimmune diseases, yet the intracellular pathways that generate the peptide antigens they recognize remain incompletely understood. Progress has been limited in part by the scarcity of reagents that directly detect defined peptide:MHC class II (pMHC-II) complexes. Here, we established an mRNA vaccine-based pipeline to generate and characterize T cell receptor (TCR)-like antibodies. One result was 1D6, a monoclonal antibody specific for NA25:A, an influenza A/PR8 neuraminidase-derived epitope presented by MHC-II. 1D6 bound NA25:A with high affinity and specificity. 1D6 recognizes NA25:A through binding determinants partially distinct from those used by the cognate TCR. Using this reagent, we confirmed the proteasome dependence of NA25 presentation and showed that NA25:A accumulates in intracellular MHC-II loading compartments without a major requirement for canonical macroautophagy, pointing to an unconventional mode of antigen presentation. These findings establish TCR-like antibodies as powerful tools for dissecting noncanonical MHC-II antigen processing pathways.
History
DepositionJun 26, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77750.png

Downloads & links

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Map

FileDownload / File: emd_77750.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.089
Minimum - Maximum-0.10436379 - 0.37989584
Average (Standard dev.)0.000070836264 (±0.008882662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_77750_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77750_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of 1D6 Fab and NA25:Ab

EntireName: Complex of 1D6 Fab and NA25:Ab
Components
  • Complex: Complex of 1D6 Fab and NA25:Ab

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Supramolecule #1: Complex of 1D6 Fab and NA25:Ab

SupramoleculeName: Complex of 1D6 Fab and NA25:Ab / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 77198
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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