+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45614 | |||||||||
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Title | T cell receptor complex | |||||||||
Map data | Main B-factor sharpened overall map | |||||||||
Sample |
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Keywords | T cell receptor T cell immunity / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / gamma-delta T cell activation / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / Fc-gamma receptor signaling pathway ...regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / gamma-delta T cell activation / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / Fc-gamma receptor signaling pathway / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / positive regulation of protein localization to cell surface / positive thymic T cell selection / signal complex assembly / Nef and signal transduction / positive regulation of cell-matrix adhesion / T cell receptor complex / smoothened signaling pathway / establishment or maintenance of cell polarity / positive regulation of interleukin-4 production / protein complex oligomerization / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / dendrite development / small molecule binding / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / FCGR activation / PD-1 signaling / Role of phospholipids in phagocytosis / T cell receptor binding / negative regulation of smoothened signaling pathway / positive regulation of T cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / cerebellum development / FCGR3A-mediated IL10 synthesis / protein tyrosine kinase binding / T cell activation / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / positive regulation of type II interferon production / positive regulation of peptidyl-tyrosine phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / cell-cell junction / protein transport / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / signaling receptor complex adaptor activity / Clathrin-mediated endocytosis / T cell receptor signaling pathway / cell body / protein-containing complex assembly / regulation of apoptotic process / adaptive immune response / dendritic spine / cell surface receptor signaling pathway / protein heterodimerization activity / G protein-coupled receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / protein kinase binding / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.01 Å | |||||||||
Authors | Gully BS / Rossjohn J | |||||||||
Funding support | Australia, 1 items
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Citation | Journal: To Be Published Title: T cell receptor complex Authors: Gully BS / Rossjohn J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45614.map.gz | 398.5 MB | EMDB map data format | |
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Header (meta data) | emd-45614-v30.xml emd-45614.xml | 33.5 KB 33.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_45614_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_45614.png | 43.3 KB | ||
Masks | emd_45614_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-45614.cif.gz | 6.9 KB | ||
Others | emd_45614_additional_1.map.gz emd_45614_additional_2.map.gz emd_45614_additional_3.map.gz emd_45614_additional_4.map.gz emd_45614_additional_5.map.gz emd_45614_half_map_1.map.gz emd_45614_half_map_2.map.gz | 398.2 MB 210.3 MB 211 MB 962.1 KB 353.2 MB 392.1 MB 392.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45614 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45614 | HTTPS FTP |
-Validation report
Summary document | emd_45614_validation.pdf.gz | 932.5 KB | Display | EMDB validaton report |
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Full document | emd_45614_full_validation.pdf.gz | 932.1 KB | Display | |
Data in XML | emd_45614_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | emd_45614_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45614 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45614 | HTTPS FTP |
-Related structure data
Related structure data | 9ci8MC 9ciaC 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_45614.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main B-factor sharpened overall map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_45614_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Local B-factor sharpened refinement of the transmembrane region
File | emd_45614_additional_1.map | ||||||||||||
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Annotation | Local B-factor sharpened refinement of the transmembrane region | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local non-sharpened refinement of the transmembrane region
File | emd_45614_additional_2.map | ||||||||||||
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Annotation | Local non-sharpened refinement of the transmembrane region | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Non-sharpened overall map
File | emd_45614_additional_3.map | ||||||||||||
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Annotation | Non-sharpened overall map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Ab initio reconstruction for the TCR extracellular domain
File | emd_45614_additional_4.map | ||||||||||||
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Annotation | Ab initio reconstruction for the TCR extracellular domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: DeepEMhancer postprocessed main map
File | emd_45614_additional_5.map | ||||||||||||
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Annotation | DeepEMhancer postprocessed main map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map A for overall map
File | emd_45614_half_map_1.map | ||||||||||||
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Annotation | Half-map A for overall map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map B for overall map
File | emd_45614_half_map_2.map | ||||||||||||
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Annotation | Half-map B for overall map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T cell receptor complex
Entire | Name: T cell receptor complex |
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Components |
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-Supramolecule #1: T cell receptor complex
Supramolecule | Name: T cell receptor complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: UCHT1 Fab
Macromolecule | Name: UCHT1 Fab / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.614113 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: MDIQMTQTTS SLSASLGDRV TISCRASQDI RNYLNWYQQK PDGTVKLLIY YTSRLHSGVP SKFSGSGSGT DYSLTISNLE QEDIATYFC QQGNTLPWTF AGGTKLEI(UNK)(UNK) RADAAPTVSI FPPASEQLTS GGASVVCFLN NFYPKSINSK WKI DGSERQ ...String: MDIQMTQTTS SLSASLGDRV TISCRASQDI RNYLNWYQQK PDGTVKLLIY YTSRLHSGVP SKFSGSGSGT DYSLTISNLE QEDIATYFC QQGNTLPWTF AGGTKLEI(UNK)(UNK) RADAAPTVSI FPPASEQLTS GGASVVCFLN NFYPKSINSK WKI DGSERQ NGVLNSWTDQ DSKDSTYSMS STLTLTKNEY ERHNSYTCEA THK(UNK)(UNK)(UNK)SPIV KSFNRS |
-Macromolecule #2: UCHT1 Fab chain 2
Macromolecule | Name: UCHT1 Fab chain 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.766975 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: EVQLQQSGPE LVKPGASMKI SCKASGYSFT GYTMNWVKQS HGKNLEWMGL INPYKGVSTY NQKFKDKATL TVDKSSSTAY MELLSLTSE DSAVYYCARS GYYGDSDWYF DVWGQGTTLT VFSAKTTPPS VYPLAPGS(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)MVTLG ...String: EVQLQQSGPE LVKPGASMKI SCKASGYSFT GYTMNWVKQS HGKNLEWMGL INPYKGVSTY NQKFKDKATL TVDKSSSTAY MELLSLTSE DSAVYYCARS GYYGDSDWYF DVWGQGTTLT VFSAKTTPPS VYPLAPGS(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)MVTLG CLVKGYFPEP VTVTWNSGSL SSGVHTFPAV LKSDLYTLSS SVTV(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)VTCNVA HPASSTTVDK KIVPR |
-Macromolecule #3: T-cell surface glycoprotein CD3 zeta chain
Macromolecule | Name: T-cell surface glycoprotein CD3 zeta chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 3.605425 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: LDPKLCYLLD GILFIYGVIL TALFLRVKFS R UniProtKB: T-cell surface glycoprotein CD3 zeta chain |
-Macromolecule #4: T-cell surface glycoprotein CD3 delta chain
Macromolecule | Name: T-cell surface glycoprotein CD3 delta 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: 11.693529 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: FKIPIEELED RVFVNCNTSI TWVEGTVGTL LSDITRLDLG KRILDPRGIY RCNGTDIYKD KESTVQVHYR MCQSCVELDP ATVAGIIVT DVIATLLLAL GVFCFA UniProtKB: T-cell surface glycoprotein CD3 delta chain |
-Macromolecule #5: T-cell surface glycoprotein CD3 epsilon chain
Macromolecule | Name: T-cell surface glycoprotein CD3 epsilon chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.111933 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: QTPYKVSISG TTVILTCPQY PGSEILWQHN DKNIGGDEDD KNIGSDEDHL SLKEFSELEQ SGYYVCYPRG SKPEDANFYL YLRARVCEN CMEMDVMSVA TIVIVDICIT GGLLLLVYYW SKNRK UniProtKB: T-cell surface glycoprotein CD3 epsilon chain |
-Macromolecule #6: T-cell surface glycoprotein CD3 gamma chain
Macromolecule | Name: T-cell surface glycoprotein CD3 gamma chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.900892 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: SIKGNHLVKV YDYQEDGSVL LTCDAEAKNI TWFKDGKMIG FLTEDKKKWN LGSNAKDPRG MYQCKGSQNK SKPLQVYYRM CQNCIELNA ATISGFLFAE IVSIFVLAVG VYFIAG UniProtKB: T-cell surface glycoprotein CD3 gamma chain |
-Macromolecule #7: T cell receptor delta constant
Macromolecule | Name: T cell receptor delta constant / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 4.104061 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: HTEKVNMMSL TVLGLRMLFA KTVAVNFLLT AKLFFL UniProtKB: T cell receptor delta constant |
-Macromolecule #8: T cell receptor gamma constant 1
Macromolecule | Name: T cell receptor gamma constant 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 4.403386 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: TLLLQLTNTS AYYMYLLLLL KSVVYFAIIT CCLLRRTA UniProtKB: T cell receptor gamma constant 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.4 / Details: Hepes buffer saline |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum ER / Energy filter - Slit width: 10 eV |
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 | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |