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Yorodumi- EMDB-41418: Cryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41418 | |||||||||
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Title | Cryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs | |||||||||
Map data | ||||||||||
Sample |
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Keywords | HLA / MHC / FAB / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information antigen processing and presentation / lumenal side of endoplasmic reticulum membrane / 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 ...antigen processing and presentation / lumenal side of endoplasmic reticulum membrane / 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 / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / positive regulation of cellular senescence / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / structural molecule activity / Golgi apparatus / cell surface / protein homodimerization activity / extracellular region / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Ross P / Adams EJ / Lodwick J / Zhao M / Slezak T / Kossiakoff A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs Authors: Ross P / Adams EJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41418.map.gz | 4.7 MB | EMDB map data format | |
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Header (meta data) | emd-41418-v30.xml emd-41418.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41418_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_41418.png | 119.2 KB | ||
Masks | emd_41418_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-41418.cif.gz | 6.4 KB | ||
Others | emd_41418_half_map_1.map.gz emd_41418_half_map_2.map.gz | 49.7 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41418 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41418 | HTTPS FTP |
-Validation report
Summary document | emd_41418_validation.pdf.gz | 655.2 KB | Display | EMDB validaton report |
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Full document | emd_41418_full_validation.pdf.gz | 654.8 KB | Display | |
Data in XML | emd_41418_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_41418_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41418 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41418 | HTTPS FTP |
-Related structure data
Related structure data | 8tnjMC 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_41418.map.gz / Format: CCP4 / Size: 64 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: 1.065 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41418_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41418_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41418_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA...
Entire | Name: Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA-B*73:01 |
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Components |
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-Supramolecule #1: Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA...
Supramolecule | Name: Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA-B*73:01 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: 9mer peptide,Beta-2-microglobulin,MHC class I antigen chimera
Macromolecule | Name: 9mer peptide,Beta-2-microglobulin,MHC class I antigen chimera 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: 49.165848 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: NRFLGDYVVG GGGSGGGGSG GGGSIQRTPK IQVYSRHPAE NGKSNFLNCY VSGFHPSDIE VDLLKNGERI EKVEHSDLSF SKDWSFYLL YYTEFTPTEK DEYACRVNHV TLSQPKIVKW DRDMGGGGSG GGGSGGGGSG GGGSGSHSMR YFHTSVSRPG R GEPRFITV ...String: NRFLGDYVVG GGGSGGGGSG GGGSIQRTPK IQVYSRHPAE NGKSNFLNCY VSGFHPSDIE VDLLKNGERI EKVEHSDLSF SKDWSFYLL YYTEFTPTEK DEYACRVNHV TLSQPKIVKW DRDMGGGGSG GGGSGGGGSG GGGSGSHSMR YFHTSVSRPG R GEPRFITV GYVDDTQFVR FDSDAASPRE EPRAPWIEQE GPEYWDRNTQ ICKAKAQTDR VGLRNLRGYY NQSEDGSHTW QT MYGCDMG PDGRLLRGYN QFAYDGKDYI ALNEDLRSWT AADTAAQITQ RKWEAARVAE QLRAYLEGEC VEWLRRHLEN GKE TLQRAD PPKTHVTHHP ISDHEATLRC WALGFYPAEI TLTWQRDGED QTQDTELVET RPAGDGTFQK WAAVVVPSGQ EQRY TCHVQ HEGLQEPLTL RWKPGGSGLE VLFQGPHHHH HHHH UniProtKB: Beta-2-microglobulin, MHC class I antigen |
-Macromolecule #2: B.8 Fab light chain
Macromolecule | Name: B.8 Fab light chain / 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: 23.523064 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSWSAYPFT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSWSAYPFT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC |
-Macromolecule #3: B.8 Fab heavy chain
Macromolecule | Name: B.8 Fab heavy chain / 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: 24.684623 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSYSIHWV RQAPGKGLEW VASISPYSGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARLIFYMWSS AMDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSYSIHWV RQAPGKGLEW VASISPYSGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARLIFYMWSS AMDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD KTHT |
-Macromolecule #4: B.1 Fab heavy chain
Macromolecule | Name: B.1 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: 25.284029 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSYYSIHWV RQAPGKGLEW VASISPYSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYSYGNSWS YDPYYGAMDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSYYSIHWV RQAPGKGLEW VASISPYSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYSYGNSWS YDPYYGAMDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTHT |
-Macromolecule #5: B.1 Fab light chain
Macromolecule | Name: B.1 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: 23.478066 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYYWAPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYYWAPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG 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
Concentration | 0.6 mg/mL | ||||||||||||
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Buffer | pH: 7.2 Component:
Details: 10 mM HEPES 150 mM NaCl 0.02% sodium azide pH 7.2 | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR Details: 10 seconds at 20 watts using Solarus 950 Plasma Cleaner System (Gatan) | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | This sample was mono-disperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 86.65 / Target criteria: EMRinger | ||||||
Output model | PDB-8tnj: |