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- EMDB-62748: Structure of anti-HEL AiTab -

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Basic information

Entry
Database: EMDB / ID: EMD-62748
TitleStructure of anti-HEL AiTab
Map data3D map
Sample
  • Complex: anti-HEL AiTab
    • Protein or peptide: H-2 class II histocompatibility antigen, A-K alpha chain
    • Protein or peptide: H-2 class II histocompatibility antigen, A-K beta chain
    • Protein or peptide: 11-72 heavy chain(V region)-mouse IgG2b CH1
    • Protein or peptide: 11-72 kappa chain(V region)-kappa chain
    • Protein or peptide: Lysozyme C
KeywordsMajor histocompatibility complex class II(MHC-II) / T cell receptor (TCR) / antigen-induced TCR-like antibodies (AiTabs) / PROTEIN BINDING
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / MHC class II protein complex binding / late endosome membrane / killing of cells of another organism / defense response to Gram-negative bacterium / adaptive immune response / early endosome / lysosome / defense response to bacterium / defense response to Gram-positive bacterium / external side of plasma membrane / lysosomal membrane / protein-containing complex binding / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular space / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / MHC classes I/II-like antigen recognition protein / : / Lysozyme-like domain superfamily / 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
Lysozyme C / H-2 class II histocompatibility antigen, A-K alpha chain / H-2 class II histocompatibility antigen, A-K beta chain
Similarity search - Component
Biological speciesMus (mice) / Mus musculus (house mouse) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsKawakami K / Yonekura K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Antigen-specific immune regulation mediated by self TCR-like antibodies
Authors: Kishida K / Kawakami K / Yonekura K / Arase H
History
DepositionDec 15, 2024-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62748.png

Downloads & links

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Map

FileDownload / File: emd_62748.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 250 pix.
= 247.5 Å		0.99 Å/pix.
x 250 pix.
= 247.5 Å		0.99 Å/pix.
x 250 pix.
= 247.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.256
Minimum - Maximum-4.754989 - 6.948775
Average (Standard dev.)-0.00045519715 (±0.08385978)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 247.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A map

Fileemd_62748_half_map_1.map
Annotationhalf_A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map

Fileemd_62748_half_map_2.map
Annotationhalf_B 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 : anti-HEL AiTab

EntireName: anti-HEL AiTab
Components
  • Complex: anti-HEL AiTab
    • Protein or peptide: H-2 class II histocompatibility antigen, A-K alpha chain
    • Protein or peptide: H-2 class II histocompatibility antigen, A-K beta chain
    • Protein or peptide: 11-72 heavy chain(V region)-mouse IgG2b CH1
    • Protein or peptide: 11-72 kappa chain(V region)-kappa chain
    • Protein or peptide: Lysozyme C

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Supramolecule #1: anti-HEL AiTab

SupramoleculeName: anti-HEL AiTab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus (mice)

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Macromolecule #1: H-2 class II histocompatibility antigen, A-K alpha chain

MacromoleculeName: H-2 class II histocompatibility antigen, A-K alpha chain
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.431785 KDa
Recombinant expressionOrganism: unidentified plasmid (others)
SequenceString:
DIEADHVGSY GITVYQSPGD IGQYTFEFDG DELFYVDLDK KETVWMLPEF AQLRRFEPQG GLQNIATGKH NLEILTKRSN STPATNEAP QATVFPKSPV LLGQPNTLIC FVDNIFPPVI NITWLRNSKS VTDGVYETSF FVNRDYSFHK LSYLTFIPSD D DIYDCKVE HWGLEEPVLK H

UniProtKB: H-2 class II histocompatibility antigen, A-K alpha chain

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Macromolecule #2: H-2 class II histocompatibility antigen, A-K beta chain

MacromoleculeName: H-2 class II histocompatibility antigen, A-K beta chain
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.124916 KDa
Recombinant expressionOrganism: unidentified plasmid (others)
SequenceString:
ERHFVHQFQP FCYFTNGTQR IRLVIRYIYN REEYVRFDSD VGEYRAVTEL GRPDAEYWNK QYLERTRAEL DTVCRHNYEK TETPTSLRR LEQPSVVISL SRTEALNHHN TLVCSVTDFY PAKIKVRWFR NGQEETVGVS STQLIRNGDW TFQVLVMLEM T PRRGEVYT CHVEHPSLKS PITVEWR

UniProtKB: H-2 class II histocompatibility antigen, A-K beta chain

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Macromolecule #3: 11-72 heavy chain(V region)-mouse IgG2b CH1

MacromoleculeName: 11-72 heavy chain(V region)-mouse IgG2b CH1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.637178 KDa
Recombinant expressionOrganism: unidentified plasmid (others)
SequenceString: DVQLQESGPG LVKPSQSLSL TCSVTGYSIT SAYYWNWIRQ FPGNKLEWMG YIRYDGSNNY NPSLKNRISI TRDTSKNQFF LKLNSVTTE DTATYYCARA YGSSYDYAMD YWGQGTSVTV SSAKTTPPSV YPLAPGCGDT TGSSVTSGCL VKGYFPEPVT V TWNSGSLS ...String:
DVQLQESGPG LVKPSQSLSL TCSVTGYSIT SAYYWNWIRQ FPGNKLEWMG YIRYDGSNNY NPSLKNRISI TRDTSKNQFF LKLNSVTTE DTATYYCARA YGSSYDYAMD YWGQGTSVTV SSAKTTPPSV YPLAPGCGDT TGSSVTSGCL VKGYFPEPVT V TWNSGSLS SSVHTFPALL QSGLYTMSSS VTVPSSTWPS QTVTCSVAHP ASSTTVDKKL

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Macromolecule #4: 11-72 kappa chain(V region)-kappa chain

MacromoleculeName: 11-72 kappa chain(V region)-kappa chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.41883 KDa
Recombinant expressionOrganism: unidentified plasmid (others)
SequenceString: DIVMTQSHKF MSTSVGDRVS ITCKASQDVG TTVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD FTLTISNVQS EDLADYFCQ QYSRYPTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
DIVMTQSHKF MSTSVGDRVS ITCKASQDVG TTVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD FTLTISNVQS EDLADYFCQ QYSRYPTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRN

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Macromolecule #5: Lysozyme C

MacromoleculeName: Lysozyme C / type: protein_or_peptide / ID: 5 / Details: HEL peptide / Number of copies: 1 / Enantiomer: LEVO / EC number: lysozyme
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 1.810984 KDa
Recombinant expressionOrganism: unidentified plasmid (others)
SequenceString:
STDYGILQIN SRWWA

UniProtKB: Lysozyme C

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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: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 98.95 e/Å2
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: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio 3D reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50032
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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