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Yorodumi- EMDB-12052: Drosophila melanogaster TRAPPCore (C1, C2, C2L, C3a/b, C4, C5, C6... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12052 | |||||||||
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Title | Drosophila melanogaster TRAPPCore (C1, C2, C2L, C3a/b, C4, C5, C6 subunits) | |||||||||
Map data | Drosophila melanogaster TRAPPCore (C1, C2, C2L, C3a, C3b, C4, C5, C6 subunits) | |||||||||
Sample |
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Keywords | Golgi / GEFS / Rab1 / TRAPP / EXOCYTOSIS | |||||||||
Function / homology | Function and homology information COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / dsRNA transport / Golgi vesicle transport / cis-Golgi network membrane / Neutrophil degranulation ...COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / dsRNA transport / Golgi vesicle transport / cis-Golgi network membrane / Neutrophil degranulation / intra-Golgi vesicle-mediated transport / cis-Golgi network / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / trans-Golgi network / spermatogenesis / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.27 Å | |||||||||
Authors | Galindo A / Munro S | |||||||||
Citation | Journal: EMBO J / Year: 2021 Title: Cryo-EM structure of metazoan TRAPPIII, the multi-subunit complex that activates the GTPase Rab1. Authors: Antonio Galindo / Vicente J Planelles-Herrero / Gianluca Degliesposti / Sean Munro / Abstract: The TRAPP complexes are nucleotide exchange factors that play essential roles in membrane traffic and autophagy. TRAPPII activates Rab11, and TRAPPIII activates Rab1, with the two complexes sharing a ...The TRAPP complexes are nucleotide exchange factors that play essential roles in membrane traffic and autophagy. TRAPPII activates Rab11, and TRAPPIII activates Rab1, with the two complexes sharing a core of small subunits that affect nucleotide exchange but being distinguished by specific large subunits that are essential for activity in vivo. Crystal structures of core subunits have revealed the mechanism of Rab activation, but how the core and the large subunits assemble to form the complexes is unknown. We report a cryo-EM structure of the entire Drosophila TRAPPIII complex. The TRAPPIII-specific subunits TRAPPC8 and TRAPPC11 hold the catalytic core like a pair of tongs, with TRAPPC12 and TRAPPC13 positioned at the joint between them. TRAPPC2 and TRAPPC2L link the core to the two large arms, with the interfaces containing residues affected by disease-causing mutations. The TRAPPC8 arm is positioned such that it would contact Rab1 that is bound to the core, indicating how the arm could determine the specificity of the complex. A lower resolution structure of TRAPPII shows a similar architecture and suggests that the TRAPP complexes evolved from a single ur-TRAPP. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12052.map.gz | 227 MB | EMDB map data format | |
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Header (meta data) | emd-12052-v30.xml emd-12052.xml | 20 KB 20 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12052_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_12052.png | 61 KB | ||
Filedesc metadata | emd-12052.cif.gz | 6.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12052 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12052 | HTTPS FTP |
-Validation report
Summary document | emd_12052_validation.pdf.gz | 661.6 KB | Display | EMDB validaton report |
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Full document | emd_12052_full_validation.pdf.gz | 661.2 KB | Display | |
Data in XML | emd_12052_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | emd_12052_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12052 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12052 | HTTPS FTP |
-Related structure data
Related structure data | 7b6dMC 7b6eC 7b6hC 7b6rC 7b6xC 7b6yC 7b6zC 7b70C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12052.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Drosophila melanogaster TRAPPCore (C1, C2, C2L, C3a, C3b, C4, C5, C6 subunits) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.248 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TRAPPIII & TRAPPII Subcomplex: TRAPPCore
Entire | Name: TRAPPIII & TRAPPII Subcomplex: TRAPPCore |
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Components |
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-Supramolecule #1: TRAPPIII & TRAPPII Subcomplex: TRAPPCore
Supramolecule | Name: TRAPPIII & TRAPPII Subcomplex: TRAPPCore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
-Macromolecule #1: Trafficking protein particle complex subunit
Macromolecule | Name: Trafficking protein particle complex subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 22.903037 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MSRQASRLDA KKVNSEFLTL TYGALVTQML RDFENAEDVN KQLERIGYNM GMRLIEDFLA RTSAPRCLEM RETADRIQQA FRIYLNIQP TISNWSPASD EFSLVFDSNP LTEFVELPPD LTNLRYSAIL SGCIRGALEM VQLEVQCWFV QDQLKGDNVT E LRVKFVRR ...String: MSRQASRLDA KKVNSEFLTL TYGALVTQML RDFENAEDVN KQLERIGYNM GMRLIEDFLA RTSAPRCLEM RETADRIQQA FRIYLNIQP TISNWSPASD EFSLVFDSNP LTEFVELPPD LTNLRYSAIL SGCIRGALEM VQLEVQCWFV QDQLKGDNVT E LRVKFVRR LEEVIPAGED LEVLFQGPVA SWSHPQFEKG AV UniProtKB: Trafficking protein particle complex subunit |
-Macromolecule #2: GEO08327p1
Macromolecule | Name: GEO08327p1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 17.59723 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MSEEILFDCL HAEIVNYCLD SNKEHDLATL EYIGFTTGYR LIERLTREVS RFKDELETMK FICTDFWMLI YKKQVDNLRT NNHGMYVVQ DKAFRFLTRI SPGTKQLEHA PKFVAFTCGL VRGALSNLGI NSTVTAEVQS IPACKFHIEV NRN UniProtKB: GEO08327p1 |
-Macromolecule #3: Trafficking protein particle complex subunit
Macromolecule | Name: Trafficking protein particle complex subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 16.990562 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MTIFNLYIFD KFGTLLHYAE WNRTKKSGIT REEEAKLTYG MLFSIKSFVS KISPHDPKEG FLYYKTNRYA LHYLETPSGL KFVLNTDTT AINVKELLQQ LYAKVWVEFV VRDPLWTPGT VVTSELFQSK LDEFVRQSPI FGIRNI UniProtKB: Trafficking protein particle complex subunit |
-Macromolecule #4: Trafficking protein particle complex subunit
Macromolecule | Name: Trafficking protein particle complex subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 24.736486 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MIIYGVYIVS KSGGLIFNLD NNVPRIEHEK TFTYPLDLVL DYDSKKVSVS FNRKDGINVG HVLVAVNGMP VNGVTLDDGR DVRTTLDAP ENYPINLKFS RPKMTTNEKI FLASMFYPLF AIASQLSPEP KSSGIEILEA DTFTLHCFQT LTGIKFIIIS E TGLNGIDL ...String: MIIYGVYIVS KSGGLIFNLD NNVPRIEHEK TFTYPLDLVL DYDSKKVSVS FNRKDGINVG HVLVAVNGMP VNGVTLDDGR DVRTTLDAP ENYPINLKFS RPKMTTNEKI FLASMFYPLF AIASQLSPEP KSSGIEILEA DTFTLHCFQT LTGIKFIIIS E TGLNGIDL LLRKVYELYS DYVLKNPFYS LEMPIRCELF DNKLQELLAQ VEKTGISNID K UniProtKB: Trafficking protein particle complex subunit |
-Macromolecule #5: Probable trafficking protein particle complex subunit 2
Macromolecule | Name: Probable trafficking protein particle complex subunit 2 type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 16.669977 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MSTYYFVIVG QNDNPIYEKE FSTVNKELRK EDHRHLTQFI AHAALDLVDE HKWKTANMQL KSIDRFNQWF VSAFITASQI RFIIVHDNK NDEGIKNFFN EMYDTYIKNS MNAFYRINTP IKSPMFEKKS EIFGRKYLLS UniProtKB: Probable trafficking protein particle complex subunit 2 |
-Macromolecule #6: Trafficking protein particle complex subunit 5
Macromolecule | Name: Trafficking protein particle complex subunit 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 22.371812 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MEKLEALKIS SMRPRSNILD RPLSKGKTEV SQSIVALLFS EIVQYSQSRV FTVPELQTRL HDLGQDVGTR IIDLYFVRER SSKRETKLT QMLLFVKTTV WKNLFGKEAE KLEHANDDER TYYIIEKEPL VNTFISVPKD KGSLNCANFT AGIVEAVLTN C GFPCKVTA ...String: MEKLEALKIS SMRPRSNILD RPLSKGKTEV SQSIVALLFS EIVQYSQSRV FTVPELQTRL HDLGQDVGTR IIDLYFVRER SSKRETKLT QMLLFVKTTV WKNLFGKEAE KLEHANDDER TYYIIEKEPL VNTFISVPKD KGSLNCANFT AGIVEAVLTN C GFPCKVTA HWHKGTTYMV KFEDFVIARD KQMEEK UniProtKB: Trafficking protein particle complex subunit 5 |
-Macromolecule #7: TRAPPC2L
Macromolecule | Name: TRAPPC2L / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 15.511826 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MAFCIAVIGK DNAPLYLTTS DMEQELELQY HVNAALDVVE EKCLIGKGAP ESKELYLGLL YSTENHKIYG FVTNTRVKFI VVIDSSNVA LRENEVRAIF RNLHLLYTDA ICNPFYIPGE SLTSKKFDRA VQKLMSGTA UniProtKB: Trafficking protein particle complex subunit 2-like protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL | ||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.001 kPa | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285.15 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | TFS KRIOS |
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Details | 32% of the images were acquiring tilted the stage 19 degrees. |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 4 / Number real images: 3671 / Average exposure time: 0.8 sec. / Average electron dose: 30.0 e/Å2 Details: 1190 from the whole dataset were collected with the stage tilted at 19 degrees |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.2 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 214.4 |
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Output model | PDB-7b6d: |