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Yorodumi- EMDB-29221: CryoEM structure of HLA-A2 MAGEA4 (286-294) in complex with H2aM3... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29221 | |||||||||
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Title | CryoEM structure of HLA-A2 MAGEA4 (286-294) in complex with H2aM31345N Fab and 2M2 Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | HLA / MHC / IMMUNE SYSTEM / antibody | |||||||||
Function / homology | Function and homology information positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / cellular response to iron ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / sensory perception of smell / MHC class I protein complex / histone deacetylase binding / negative regulation of neurogenesis / multicellular organismal-level iron ion homeostasis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Modulation by Mtb of host immune system / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
Authors | Saotome K / Franklin MC | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: CryoEM structure of HLA-A2 MAGEA4 (286-294) in complex with H2aM31345N Fab Authors: Saotome K / Franklin MC | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29221.map.gz | 147.7 MB | EMDB map data format | |
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Header (meta data) | emd-29221-v30.xml emd-29221.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_29221.png | 83.7 KB | ||
Filedesc metadata | emd-29221.cif.gz | 5.8 KB | ||
Others | emd_29221_half_map_1.map.gz emd_29221_half_map_2.map.gz | 141 MB 140.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29221 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29221 | HTTPS FTP |
-Validation report
Summary document | emd_29221_validation.pdf.gz | 787 KB | Display | EMDB validaton report |
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Full document | emd_29221_full_validation.pdf.gz | 786.6 KB | Display | |
Data in XML | emd_29221_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | emd_29221_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29221 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29221 | HTTPS FTP |
-Related structure data
Related structure data | 8fjbMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29221.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_29221_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29221_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HLA-A2 MAGEA4 (286-294) complex with H2aM31345N Fab and 2M2 Fab
Entire | Name: HLA-A2 MAGEA4 (286-294) complex with H2aM31345N Fab and 2M2 Fab |
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Components |
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-Supramolecule #1: HLA-A2 MAGEA4 (286-294) complex with H2aM31345N Fab and 2M2 Fab
Supramolecule | Name: HLA-A2 MAGEA4 (286-294) complex with H2aM31345N Fab and 2M2 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: MHC class I antigen, Beta-2-microglobulin
Supramolecule | Name: MHC class I antigen, Beta-2-microglobulin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Melanoma-associated antigen 4 peptide
Supramolecule | Name: Melanoma-associated antigen 4 peptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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-Supramolecule #4: H2aM31345N Fab heavy chain, H2aM31345N Fab light chain
Supramolecule | Name: H2aM31345N Fab heavy chain, H2aM31345N Fab light chain type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: MHC class I antigen
Macromolecule | Name: MHC class I antigen / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 32.082512 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSHSMRYFF TSVSRPGRGE PRFIAVGYVD DTQFVRFDSD AASQRMEPRA PWIEQEGPEY WDGETRKVKA HSQTHRVDLG TLRGYYNQS EAGSHTVQRM YGCDVGSDWR FLRGYHQYAY DGKDYIALKE DLRSWTAADM AAQTTKHKWE AAHVAEQLRA Y LEGTCVEW ...String: MGSHSMRYFF TSVSRPGRGE PRFIAVGYVD DTQFVRFDSD AASQRMEPRA PWIEQEGPEY WDGETRKVKA HSQTHRVDLG TLRGYYNQS EAGSHTVQRM YGCDVGSDWR FLRGYHQYAY DGKDYIALKE DLRSWTAADM AAQTTKHKWE AAHVAEQLRA Y LEGTCVEW LRRYLENGKE TLQRTDAPKT HMTHHAVSDH EATLRCWALS FYPAEITLTW QRDGEDQTQD TELVETRPAG DG TFQKWAA VVVPSGQEQR YTCHVQHEGL PKPLTLRWEP UniProtKB: MHC class I antigen |
-Macromolecule #2: Beta-2-microglobulin
Macromolecule | Name: Beta-2-microglobulin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.879356 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIQRTPKIQV YSRHPAENGK SNFLNCYVSG FHPSDIEVDL LKNGERIEKV EHSDLSFSKD WSFYLLYYTE FTPTEKDEYA CRVNHVTLS QPKIVKWDRD M UniProtKB: Beta-2-microglobulin |
-Macromolecule #3: Melanoma-associated antigen 4 peptide
Macromolecule | Name: Melanoma-associated antigen 4 peptide / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.08133 KDa |
Sequence | String: KVLEHVVRV UniProtKB: Melanoma-associated antigen 8 |
-Macromolecule #4: H2aM31345N Fab heavy chain
Macromolecule | Name: H2aM31345N Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.831629 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: QVQLVESGGG LVKPGGSLRL SCAASGFTFS EYYMTWIRQA PGQGLEWVSY ISSSGFNIYY ADSVKGRFTI SRDNAKNSLF LQMNSLRVE DTAVYYCARE GVTDGMDVWG QGTTVTVSSA STKGPSVFPL APCSRSTSES TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String: QVQLVESGGG LVKPGGSLRL SCAASGFTFS EYYMTWIRQA PGQGLEWVSY ISSSGFNIYY ADSVKGRFTI SRDNAKNSLF LQMNSLRVE DTAVYYCARE GVTDGMDVWG QGTTVTVSSA STKGPSVFPL APCSRSTSES TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTKT YTCNVDHKPS NTKVDKRVES KYGPP |
-Macromolecule #5: H2aM31345N Fab light chain
Macromolecule | Name: H2aM31345N Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.438967 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93015 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |