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- EMDB-70276: CryoEM structure of anti-MHC-I mAb B1.23.2 Fc domains -

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Basic information

Entry
Database: EMDB / ID: EMD-70276
TitleCryoEM structure of anti-MHC-I mAb B1.23.2 Fc domains
Map datastructure of anti-MHC-I mAb B1.23.2 Fc domains
Sample
  • Complex: Complex of Anti-human-mAb B1.23.2 and MHC-I HLA-B44:05, Fc domains
    • Protein or peptide: Anti-MHC-I mAb B1.23.2 Fc domains H-chain
KeywordsMHC-I / HLA / anti-human-mAb / H2-Dd / B1.23.2 / anti-MHC-I antibody / anti-tumor / cancer immunotherapy / ANTITUMOR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsJiang J / Natarajan K / Margulies DH / Huang R
Funding support United States, 1 items
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 Fc domains
Authors: Jiang J / Natarajan K / Margulies DH
History
DepositionApr 20, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70276.png

Downloads & links

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Map

FileDownload / File: emd_70276.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of anti-MHC-I mAb B1.23.2 Fc domains
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.46996394 - 0.707019
Average (Standard dev.)0.001325534 (±0.012280459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_70276_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_70276_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Anti-human-mAb B1.23.2 and MHC-I HLA-B44:05, Fc domains

EntireName: Complex of Anti-human-mAb B1.23.2 and MHC-I HLA-B44:05, Fc domains
Components
  • Complex: Complex of Anti-human-mAb B1.23.2 and MHC-I HLA-B44:05, Fc domains
    • Protein or peptide: Anti-MHC-I mAb B1.23.2 Fc domains H-chain

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Supramolecule #1: Complex of Anti-human-mAb B1.23.2 and MHC-I HLA-B44:05, Fc domains

SupramoleculeName: Complex of Anti-human-mAb B1.23.2 and MHC-I HLA-B44:05, Fc domains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The sample was mixed 1:1 mole ratio of antibody and HLA-B44 and purified. with concentration of 1.0 mg/ml
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 196.472 KDa

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Macromolecule #1: Anti-MHC-I mAb B1.23.2 Fc domains H-chain

MacromoleculeName: Anti-MHC-I mAb B1.23.2 Fc domains H-chain / type: protein_or_peptide / ID: 1
Details: mAb B1.23.2 full-length: VH, human IgG1 CH1, Fc (CH2,CH3) domains, including the hinge 9213-226), and LALAPG mutations (A230, A231, and G325)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Cell: Expi293F
Molecular weightTheoretical: 48.506445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQSGTV LARPGSSVKM SCKASGYSFT SYWMHWVKQR PGQGLEWIGA IYPGNSDATY NQKFKGKAKL TAVTSANTAY MELSSLTNE DSAVYYCTNY FDQWGQGTTL TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL T SGVHTFPA ...String:
QVQLQQSGTV LARPGSSVKM SCKASGYSFT SYWMHWVKQR PGQGLEWIGA IYPGNSDATY NQKFKGKAKL TAVTSANTAY MELSSLTNE DSAVYYCTNY FDQWGQGTTL TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL T SGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THTCPPCPAP EAAGGPSVFL FP PKPKDTL MISRTPEVTC VVVDVSHEDP EVKFNWYVDG VEVHNAKTKP REEQYNSTYR VVSVLTVLHQ DWLNGKEYKC KVS NKALGA PIEKTISKAK GQPREPQVYT LPPSREEMTK NQVSLTCLVK GFYPSDIAVE WESNGQPENN YKTTPPVLDS DGSF FLYSK LTVDKSRWQQ GNVFSCSVMH EALHNHYTQK SLSLSPGK

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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

Concentration1.0 mg/mL
BufferpH: 8 / Component - Concentration: 0.25 mg/ml / Component - Name: TBS / Details: TBS, 0.25 mg/ml
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 78.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 7154 / Average exposure time: 2.5 sec. / Average electron dose: 54.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 60096 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 664724
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Details: PATCH CTF estimation / Type: NONE
Startup modelType of model: OTHER / Details: Alphafold3 with manual modification
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 251084
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 50 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 92.8 / Target criteria: CC
Output model

PDB-9oa9:
CryoEM structure of anti-MHC-I mAb B1.23.2 Fc domains

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