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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12060 | |||||||||
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Title | TRAPPC11 region from the MiniTRAPPIII complex | |||||||||
![]() | C11 region from MiniTRAPPIII complex | |||||||||
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Function / homology | ![]() RAB GEFs exchange GTP for GDP on RABs / TRAPPIII protein complex / Golgi vesicle transport / protein secretion / intracellular transport / long-term memory / Golgi apparatus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||
![]() | Galindo A / Munro S / Planelles-Herrero VJ | |||||||||
![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 228.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.5 KB 13.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 194.7 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 384.7 KB | Display | ![]() |
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Full document | ![]() | 384.3 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b6zMC ![]() 7b6dC ![]() 7b6eC ![]() 7b6hC ![]() 7b6rC ![]() 7b6xC ![]() 7b6yC ![]() 7b70C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | C11 region from MiniTRAPPIII complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2564 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : TRAPPC11 region from the Mini TRAPPIII complex.
Entire | Name: TRAPPC11 region from the Mini TRAPPIII complex. |
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Components |
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-Supramolecule #1: TRAPPC11 region from the Mini TRAPPIII complex.
Supramolecule | Name: TRAPPC11 region from the Mini TRAPPIII complex. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Trafficking protein particle complex subunit 11
Macromolecule | Name: Trafficking protein particle complex subunit 11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 81.847164 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MTMDATALPS ELLVTPQPLV GFCGLDTARV SVHKAVWEAF SGSLQRKAAD RAAVQYKLLP PNYEFPVAKP KRASYEWYHP KGILKRNWM LKHLHVLPSV VVLFQDMEWN DLQWTEKQVQ CAAIVQALKN TLQERNTRLC LVLLQRAAPL PPGEDLLAAE R AASLTNAC ...String: MTMDATALPS ELLVTPQPLV GFCGLDTARV SVHKAVWEAF SGSLQRKAAD RAAVQYKLLP PNYEFPVAKP KRASYEWYHP KGILKRNWM LKHLHVLPSV VVLFQDMEWN DLQWTEKQVQ CAAIVQALKN TLQERNTRLC LVLLQRAAPL PPGEDLLAAE R AASLTNAC GITSKMLFIL PHTEHLTGYA LRLESAFLDM AQSYYALMSK RIRNHRDQLT AAHTSLKIRH QFKLGFVAEM RQ DFSTGQK HYFQAYANLD EIRINDGNCL EIKTLAGFLN YKICRLMFKL KTPRDAINQF IIHVEKHKSR VGFKDLAFEH HAW LSTQHS VFAELFCEAI KNGLPALQTQ HPGIYYHKAA EFVMKRRDAA MEAYAAMQAS SEATPTPIQN PLSLYTEFFG IRAV KTGDL VAEQQANMQL CDQERSYNHS AAIIALLSQA MAQFKIYKCL RFRKKLAIDM AEEYLKSGDH AKALTLYSLM LPDYR QEKW TTIFTDVLLK TLRCALLSGS VADYIACSVE ALSLRHQSDQ SERILILENL WQVFQGVPPM PKTQLTPEAQ ALWTSA LAN VKSPIQIDLD KVNDVVEMCA TFERVQLSND DLLQLQLIVR VLTDIPLRIR SFHVILADAG NPQNSYKLEA LKYFCFP TL TQLRGQKQPD DEQLENPSQE PKNFEKNMRL EPGSYYQLFC STEAQQFHEN TQLRIVRLEA HMGTDQVAAL LTCSSN |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 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 - Atmosphere: AIR / Pretreatment - Pressure: 0.001 kPa | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285.15 K / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3443 / Average exposure time: 12.0 sec. / Average electron dose: 45.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0025 µm / Nominal defocus min: 0.0015 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | ![]() PDB-7b6z: |