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- PDB-9l1l: Structure of anti-HEL AiTab -

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Basic information

Entry
Database: PDB / ID: 9l1l
TitleStructure of anti-HEL AiTab
Components
  • 11-72 heavy chain(V region)-mouse IgG2b CH1
  • 11-72 kappa chain(V region)-kappa chain
  • H-2 class II histocompatibility antigen, A-K alpha chain
  • H-2 class II histocompatibility antigen, A-K beta chain
  • Lysozyme C
KeywordsPROTEIN BINDING / Major histocompatibility complex class II(MHC-II) / T cell receptor (TCR) / antigen-induced TCR-like antibodies (AiTabs)
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 musculus (house mouse)
Gallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsKawakami, K. / Yonekura, K.
Funding support Japan, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 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: H-2 class II histocompatibility antigen, A-K alpha chain
B: H-2 class II histocompatibility antigen, A-K beta chain
C: 11-72 heavy chain(V region)-mouse IgG2b CH1
D: 11-72 kappa chain(V region)-kappa chain
P: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)91,4245
Polymers91,4245
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 20431.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: unidentified plasmid (others) / References: UniProt: P01910
#2: Protein H-2 class II histocompatibility antigen, A-K beta chain


Mass: 22124.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1 / Production host: unidentified plasmid (others) / References: UniProt: P06343
#3: Antibody 11-72 heavy chain(V region)-mouse IgG2b CH1


Mass: 23637.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: unidentified plasmid (others)
#4: Antibody 11-72 kappa chain(V region)-kappa chain


Mass: 23418.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: unidentified plasmid (others)
#5: Protein/peptide Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 1810.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HEL peptide / Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: unidentified plasmid (others) / References: UniProt: P00698, lysozyme
Has protein modificationY

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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: anti-HEL AiTab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus (mice)
Source (recombinant)Organism: unidentified plasmid (others)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 98.95 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50032 / Symmetry type: POINT

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