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- EMDB-46600: CryoEM structure of anti-MHC-I Fab M1/42 complex with H2-Dd -

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Basic information

Entry
Database: EMDB / ID: EMD-46600
TitleCryoEM structure of anti-MHC-I Fab M1/42 complex with H2-Dd
Map datamain map file
Sample
  • Complex: Complex of Anti mouse Fab M1/42 and MHC-I H2-Dd
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Fab M1/42 Light Chain
    • Protein or peptide: Surface protein gp120
    • Protein or peptide: H-2 class I histocompatibility antigen, D-D alpha chain
    • Protein or peptide: Fab M1/42 Heavy Chain
KeywordsMHC-I / anti-mouse-mAb / H2-Dd / M1/42 / anti-MHC-I antibody / anti-tumor / cancer immunotherapy / ANTITUMOR PROTEIN / ANTITUMOR PROTEIN-Immune System complex
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / positive regulation of plasma membrane raft polarization ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / Neutrophil degranulation / host cell endosome membrane / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / iron ion transport / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / 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 / MHC class I protein complex / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / viral protein processing / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsJiang J / Natarajan K / Margulies DH / Lei H / 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 Fab M1/42 complex with H2-Dd
Authors: Jiang J / Natarajan K / Margulies DH
History
DepositionAug 16, 2024-
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_46600.png

Downloads & links

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Map

FileDownload / File: emd_46600.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map file
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: 0.06
Minimum - Maximum-0.19335185 - 0.4093269
Average (Standard dev.)0.000690802 (±0.010730638)
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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Mask #1

Fileemd_46600_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_46600_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_46600_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 mouse Fab M1/42 and MHC-I H2-Dd

EntireName: Complex of Anti mouse Fab M1/42 and MHC-I H2-Dd
Components
  • Complex: Complex of Anti mouse Fab M1/42 and MHC-I H2-Dd
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Fab M1/42 Light Chain
    • Protein or peptide: Surface protein gp120
    • Protein or peptide: H-2 class I histocompatibility antigen, D-D alpha chain
    • Protein or peptide: Fab M1/42 Heavy Chain

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Supramolecule #1: Complex of Anti mouse Fab M1/42 and MHC-I H2-Dd

SupramoleculeName: Complex of Anti mouse Fab M1/42 and MHC-I H2-Dd / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The sample was mixed 1:1 mole ratio of Fab and H2-Dd and purified. with concentration of 1.0 mg/ml
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 90.129 KDa

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Macromolecule #1: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.529153 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
IQKTPQIQVY SRHPPENGKP NILNCYVTQF HPPHIEIQML KNGKKIPKVE MSDMSFSKDW SFYILAHTEF TPTETDTYAC RVKHASMAE PKTVYWDRD

UniProtKB: Beta-2-microglobulin

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Macromolecule #2: Fab M1/42 Light Chain

MacromoleculeName: Fab M1/42 Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 23.555971 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS MSASLGDKVT INCLASEDIG NYLSWYQQRP GKSPKLMIYG VTNLEDGVPS RFSGSRSGSD YSLTINSLGY DDEGIYHCH EYYEYPFTFG SGTKLEIKRA DAAPTVSIFP PSTEQLATGG ASVVCLMNNF YPRDISVKWK IDGTERRDGV L DSVTDQDS ...String:
DIQMTQSPSS MSASLGDKVT INCLASEDIG NYLSWYQQRP GKSPKLMIYG VTNLEDGVPS RFSGSRSGSD YSLTINSLGY DDEGIYHCH EYYEYPFTFG SGTKLEIKRA DAAPTVSIFP PSTEQLATGG ASVVCLMNNF YPRDISVKWK IDGTERRDGV L DSVTDQDS KDSTYSMSST LSLTKADYES HNLYTCEVVH KTSSSPVVKS FNRNE

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Macromolecule #3: Surface protein gp120

MacromoleculeName: Surface protein gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.075265 KDa
SequenceString:
RGPGRAFVTI

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #4: H-2 class I histocompatibility antigen, D-D alpha chain

MacromoleculeName: H-2 class I histocompatibility antigen, D-D alpha chain
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 31.819361 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SHSLRYFVTA VSRPGFGEPR YMEVGYVDNT EFVRFDSDAE NPRYEPRARW IEQEGPEYWE RETRRAKGNE QSFRVDLRTA LRYYNQSAG GSHTLQWMAG CDVESDGRLL RGYWQFAYDG CDYIALNEDL KTWTAADMAA QITRRKWEQA GAAERDRAYL E GECVEWLR ...String:
SHSLRYFVTA VSRPGFGEPR YMEVGYVDNT EFVRFDSDAE NPRYEPRARW IEQEGPEYWE RETRRAKGNE QSFRVDLRTA LRYYNQSAG GSHTLQWMAG CDVESDGRLL RGYWQFAYDG CDYIALNEDL KTWTAADMAA QITRRKWEQA GAAERDRAYL E GECVEWLR RYLKNGNATL LRTDPPKAHV THHRRPEGDV TLRCWALGFY PADITLTWQL NGEELTQEME LVETRPAGDG TF QKWASVV VPLGKEQKYT CHVEHEGLPE PLTLRW

UniProtKB: H-2 class I histocompatibility antigen, D-D alpha chain

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Macromolecule #5: Fab M1/42 Heavy Chain

MacromoleculeName: Fab M1/42 Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 23.754752 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVTLKESGPG MLQPSKTLSL TCSFSGFSLS TSGLVVNWIR QPSGKSLEWL AAIDWDGDEY YNPSPKSRLT VSKDTSNTQV FLKITSVDT VDTATYYCAR SRRYGRYSGA FDYWGLGVMV TVSSAETTAP SVYPLAPGTA LKSNSMVTLG CLVKGYFPEP V TVTWNSGA ...String:
QVTLKESGPG MLQPSKTLSL TCSFSGFSLS TSGLVVNWIR QPSGKSLEWL AAIDWDGDEY YNPSPKSRLT VSKDTSNTQV FLKITSVDT VDTATYYCAR SRRYGRYSGA FDYWGLGVMV TVSSAETTAP SVYPLAPGTA LKSNSMVTLG CLVKGYFPEP V TVTWNSGA LSSGVHTFPA VLQSGLYTLT SSVTVPSSTW SSQAVTCNVA HPASSTKVDK KIVP

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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
GridModel: EMS Lacey Carbon / 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

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 2993 / 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: 735810
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Details: PATCH CTF estimation / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8tq4

Final reconstructionNumber classes used: 41 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 320842
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 41 / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8tq4


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 146.2 / Target criteria: CC
Output model

PDB-9d72:
CryoEM structure of anti-MHC-I Fab M1/42 complex with H2-Dd

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