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- EMDB-53299: Cryo-EM structure of the SN230G6 Fab - HLA-A*02:01 human alloanti... -

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Basic information

Entry
Database: EMDB / ID: EMD-53299
TitleCryo-EM structure of the SN230G6 Fab - HLA-A*02:01 human alloantibody-HLA complex
Map data
Sample
  • Complex: SN230G6 - HLA-A*02:01
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Peptide VLHDDLLEA
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: SN230G6 Fab Heavy Chain
    • Protein or peptide: SN230G6 Fab Light Chain
KeywordsHuman Leucocyte Antigens / Alloantibody / Antibody / Antigen / Epitope / protein-protein interaction / organ rejection / IMMUNE SYSTEM
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion ...antigen processing and presentation of peptide antigen via MHC class I / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / 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 / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / 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 exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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. ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsZampieri V / Priddey A / Schneider S / Heidt S / Kosmoliaptsis V / Marquez JA
Funding supportEuropean Union, United Kingdom, United States, 5 items
OrganizationGrant numberCountry
European Union (EU)101094131European Union
European Union (EU)847543European Union
National Institute for Health and Care Research (NIHR)PDF-2016-09-065 United Kingdom
NIHR Blood and Transplant Research Unit in Organ Donation and TransplantationNIHR203332 United Kingdom
Terasaki InstituteG106170 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the SN230G6 Fab - HLA-A*02:01 human alloantibody-HLA complex
Authors: Zampieri V / Priddey A / Schneider S / Heidt S / Kosmoliaptsis V / Marquez JA
History
DepositionMar 31, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53299.png

Downloads & links

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Map

FileDownload / File: emd_53299.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 300 pix.
= 244.2 Å		0.81 Å/pix.
x 300 pix.
= 244.2 Å		0.81 Å/pix.
x 300 pix.
= 244.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.814 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.41408652 - 0.7599518
Average (Standard dev.)-0.0007037387 (±0.013274747)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 244.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53299_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53299_half_map_2.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 : SN230G6 - HLA-A*02:01

EntireName: SN230G6 - HLA-A*02:01
Components
  • Complex: SN230G6 - HLA-A*02:01
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Peptide VLHDDLLEA
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: SN230G6 Fab Heavy Chain
    • Protein or peptide: SN230G6 Fab Light Chain

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Supramolecule #1: SN230G6 - HLA-A*02:01

SupramoleculeName: SN230G6 - HLA-A*02:01 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: MHC class I antigen

MacromoleculeName: MHC class I antigen / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.854203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASQRMEPRAP WIEQEGPEYW DGETRKVKAH SQTHRVDLGT LRGYYNQSE AGSHTVQRMY GCDVGSDWRF LRGYHQYAYD GKDYIALKED LRSWTAADMA AQTTKHKWEA AHVAEQLRAY L EGTCVEWL ...String:
GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASQRMEPRAP WIEQEGPEYW DGETRKVKAH SQTHRVDLGT LRGYYNQSE AGSHTVQRMY GCDVGSDWRF LRGYHQYAYD GKDYIALKED LRSWTAADMA AQTTKHKWEA AHVAEQLRAY L EGTCVEWL RRYLENGKET LQRTDAPKTH MTHHAVSDHE ATLRCWALSF YPAEITLTWQ RDGEDQTQDT ELVETRPAGD GT FQKWAAV VVPSGQEQRY TCHVQHEGLP KPLTLRWE

UniProtKB: MHC class I antigen

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Macromolecule #2: Peptide VLHDDLLEA

MacromoleculeName: Peptide VLHDDLLEA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.025133 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VLHDDLLEA

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Macromolecule #3: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.879356 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MIQRTPKIQV YSRHPAENGK SNFLNCYVSG FHPSDIEVDL LKNGERIEKV EHSDLSFSKD WSFYLLYYTE FTPTEKDEYA CRVNHVTLS QPKIVKWDRD M

UniProtKB: Beta-2-microglobulin

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Macromolecule #4: SN230G6 Fab Heavy Chain

MacromoleculeName: SN230G6 Fab Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.637834 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EAQLVESGGG LVKPGGSLRL SCAASGFAFA NHTMNWVRQA PGKGLEWVSS ISISSTYIYY ADSVKGRFSI SRDNAKNSLY LQMNSLKAE DTAVYYCARD RPPLRIVGIW DYWGQGILVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
EAQLVESGGG LVKPGGSLRL SCAASGFAFA NHTMNWVRQA PGKGLEWVSS ISISSTYIYY ADSVKGRFSI SRDNAKNSLY LQMNSLKAE DTAVYYCARD RPPLRIVGIW DYWGQGILVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HHHHHHHHHH

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Macromolecule #5: SN230G6 Fab Light Chain

MacromoleculeName: SN230G6 Fab Light Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.903186 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSA SGTPGQRVTI SCSGSSANIG SNIVDWYQHL PGTAPKLLIY SDNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC VAWDDSRYGY VFGTGTRVTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSVLTQPPSA SGTPGQRVTI SCSGSSANIG SNIVDWYQHL PGTAPKLLIY SDNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC VAWDDSRYGY VFGTGTRVTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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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 mg/mL
BufferpH: 7.4 / Details: 1X Phosphate-Buffered Saline (PBS)
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Number real images: 12891 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 408487
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4u6x

chain_id: A, source_name: PDB, initial_model_type: experimental model

4u6x

chain_id: B, source_name: PDB, initial_model_type: experimental model
chain_id: L, source_name: AlphaFold, initial_model_type: in silico model
chain_id: H, source_name: AlphaFold, initial_model_type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9qqe:
Cryo-EM structure of the SN230G6 Fab - HLA-A*02:01 human alloantibody-HLA complex

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