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- PDB-9d73: CryoEM structure of anti-MHC-I mAb B1.23.2 complex with HLA-B44:05 -

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Basic information

Entry
Database: PDB / ID: 9d73
TitleCryoEM structure of anti-MHC-I mAb B1.23.2 complex with HLA-B44:05
Components
  • B1.23.2 Light Chain: VL and C kappa domains
  • B1.23.2 mAb Heavy Chain: Full-length
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05)
  • MHC class II antigen peptide
KeywordsANTITUMOR PROTEIN/Immune System / MHC-I / anti-human-mAb / H2-Dd / B1.23.2 / anti-MHC-I antibody / anti-tumor / cancer immunotherapy / ANTITUMOR PROTEIN / ANTITUMOR PROTEIN-Immune System complex
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of iron ion transport / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / Endosomal/Vacuolar pathway ...antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of iron ion transport / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / peptide antigen binding / positive regulation of T cell activation / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...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 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / 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
Beta-2-microglobulin / MHC class I antigen / MHC class II antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsJiang, J. / Natarajan, K. / Lei, H. / Huang, R. / Margulies, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Intramural United States
CitationJournal: To Be Published
Title: CryoEM structure of anti-MHC-I B1.23.2 complex with HLA-B44:05
Authors: Jiang, J. / Natarajan, K. / Margulies, D.H.
History
DepositionAug 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 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

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05)
B: Beta-2-microglobulin
P: MHC class II antigen peptide
H: B1.23.2 mAb Heavy Chain: Full-length
L: B1.23.2 Light Chain: VL and C kappa domains


Theoretical massNumber of molelcules
Total (without water)117,1255
Polymers117,1255
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 HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05)


Mass: 31802.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q860B7
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide MHC class II antigen peptide


Mass: 1090.165 Da / Num. of mol.: 1
Fragment: HLA-DPA1*02:01 derived peptide 77-85 (UNP residues 36-44)
Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q9TQB0
#4: Antibody B1.23.2 mAb Heavy Chain: Full-length


Mass: 48506.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: B1.23.2 mAb VH, CH1 of human IgG1, and CH2, CH3 domains, including the hinge (213-226) and LALAPG mutations (A230, A231, and G325)
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCDNA3.1 / Cell (production host): Expi293F / Production host: Homo sapiens (human)
#5: Antibody B1.23.2 Light Chain: VL and C kappa domains


Mass: 23846.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCDNA3.1 / Cell (production host): Expi293F / Production host: Homo sapiens (human)
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: Complex of Anti-human-mAb B1.23.2 and MHC-I HLA-B44:05
Type: COMPLEX
Details: The sample was mixed 1:1 mole ratio of antibody and HLA-B44 and purified. with concentration of 1.0 mg/ml
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.196472 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F / Plasmid: pCDNA3.1
Buffer solutionpH: 8
Buffer componentConc.: 0.25 mg/ml / Name: TBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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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 magnification: 105000 X / Calibrated magnification: 60096 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 78 K
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 54.2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7154
Image scansSampling size: 5.001 µm / Movie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2SerialEM3.8-4.0image acquisition
4cryoSPARC4.4.1CTF correction
7UCSF ChimeraX1.7.1model fitting
11cryoSPARC4.4.1classification
12cryoSPARC4.4.13D reconstruction
13PHENIX1.19.2-4158model refinement
CTF correctionDetails: PATCH CTF estimation / Type: NONE
Particle selectionNum. of particles selected: 664724
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 359876 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Num. of class averages: 48 / Symmetry type: POINT
Atomic model buildingB value: 128.8 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: CC
Atomic model buildingPDB-ID: 8TQ6

8tq6


Accession code: 8TQ6 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.02 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036471
ELECTRON MICROSCOPYf_angle_d0.6068801
ELECTRON MICROSCOPYf_dihedral_angle_d5.621903
ELECTRON MICROSCOPYf_chiral_restr0.041949
ELECTRON MICROSCOPYf_plane_restr0.0031141

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