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- EMDB-12052: Drosophila melanogaster TRAPPCore (C1, C2, C2L, C3a/b, C4, C5, C6... -

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Basic information

Entry
Database: EMDB / ID: EMD-12052
TitleDrosophila melanogaster TRAPPCore (C1, C2, C2L, C3a/b, C4, C5, C6 subunits)
Map dataDrosophila melanogaster TRAPPCore (C1, C2, C2L, C3a, C3b, C4, C5, C6 subunits)
Sample
  • Complex: TRAPPIII & TRAPPII Subcomplex: TRAPPCore
    • Protein or peptide: Trafficking protein particle complex subunit
    • Protein or peptide: GEO08327p1
    • Protein or peptide: Trafficking protein particle complex subunit
    • Protein or peptide: Trafficking protein particle complex subunit
    • Protein or peptide: Probable trafficking protein particle complex subunit 2
    • Protein or peptide: Trafficking protein particle complex subunit 5
    • Protein or peptide: TRAPPC2L
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 / Neutrophil degranulation / intra-Golgi vesicle-mediated transport ...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 / Neutrophil degranulation / intra-Golgi vesicle-mediated transport / cis-Golgi network / cis-Golgi network membrane / 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
Trafficking protein particle complex subunit 2-like / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / Trafficking protein particle complex subunit / Sybindin-like family / Sybindin-like family / TRAPP I complex, subunit 5 / TRAPP complex, Trs33 subunit / Bet3 family / Transport protein particle (TRAPP) component ...Trafficking protein particle complex subunit 2-like / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / Trafficking protein particle complex subunit / Sybindin-like family / Sybindin-like family / TRAPP I complex, subunit 5 / TRAPP complex, Trs33 subunit / Bet3 family / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / NO signalling/Golgi transport ligand-binding domain superfamily / Longin-like domain superfamily
Similarity search - Domain/homology
Trafficking protein particle complex subunit 2-like protein / Trafficking protein particle complex subunit 5 / Trafficking protein particle complex subunit / GEO08327p1 / Trafficking protein particle complex subunit / Trafficking protein particle complex subunit / Probable trafficking protein particle complex subunit 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.27 Å
AuthorsGalindo A / Munro S / Planelles-Herrero VJ / Degliesposti G
CitationJournal: 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
DepositionDec 7, 2020-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b6d
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12052.png

Downloads & links

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Map

FileDownload / File: emd_12052.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDrosophila melanogaster TRAPPCore (C1, C2, C2L, C3a, C3b, C4, C5, C6 subunits)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 400 pix.
= 499.2 Å		1.25 Å/pix.
x 400 pix.
= 499.2 Å		1.25 Å/pix.
x 400 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.248 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.036 / Movie #1: 0.036
Minimum - Maximum-0.029665515 - 0.10199049
Average (Standard dev.)-0.00022892337 (±0.0029885916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 499.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2481.2481.248
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z499.200499.200499.200
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0300.102-0.000

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Supplemental data

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Sample components

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Entire : TRAPPIII & TRAPPII Subcomplex: TRAPPCore

EntireName: TRAPPIII & TRAPPII Subcomplex: TRAPPCore
Components
  • Complex: TRAPPIII & TRAPPII Subcomplex: TRAPPCore
    • Protein or peptide: Trafficking protein particle complex subunit
    • Protein or peptide: GEO08327p1
    • Protein or peptide: Trafficking protein particle complex subunit
    • Protein or peptide: Trafficking protein particle complex subunit
    • Protein or peptide: Probable trafficking protein particle complex subunit 2
    • Protein or peptide: Trafficking protein particle complex subunit 5
    • Protein or peptide: TRAPPC2L

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Supramolecule #1: TRAPPIII & TRAPPII Subcomplex: TRAPPCore

SupramoleculeName: TRAPPIII & TRAPPII Subcomplex: TRAPPCore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)

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Macromolecule #1: Trafficking protein particle complex subunit

MacromoleculeName: Trafficking protein particle complex subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 22.903037 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: 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

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Macromolecule #2: GEO08327p1

MacromoleculeName: GEO08327p1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 17.59723 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString:
MSEEILFDCL HAEIVNYCLD SNKEHDLATL EYIGFTTGYR LIERLTREVS RFKDELETMK FICTDFWMLI YKKQVDNLRT NNHGMYVVQ DKAFRFLTRI SPGTKQLEHA PKFVAFTCGL VRGALSNLGI NSTVTAEVQS IPACKFHIEV NRN

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Macromolecule #3: Trafficking protein particle complex subunit

MacromoleculeName: Trafficking protein particle complex subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 16.990562 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString:
MTIFNLYIFD KFGTLLHYAE WNRTKKSGIT REEEAKLTYG MLFSIKSFVS KISPHDPKEG FLYYKTNRYA LHYLETPSGL KFVLNTDTT AINVKELLQQ LYAKVWVEFV VRDPLWTPGT VVTSELFQSK LDEFVRQSPI FGIRNI

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Macromolecule #4: Trafficking protein particle complex subunit

MacromoleculeName: Trafficking protein particle complex subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 24.736486 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: 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

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Macromolecule #5: Probable trafficking protein particle complex subunit 2

MacromoleculeName: Probable trafficking protein particle complex subunit 2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 16.669977 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString:
MSTYYFVIVG QNDNPIYEKE FSTVNKELRK EDHRHLTQFI AHAALDLVDE HKWKTANMQL KSIDRFNQWF VSAFITASQI RFIIVHDNK NDEGIKNFFN EMYDTYIKNS MNAFYRINTP IKSPMFEKKS EIFGRKYLLS

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Macromolecule #6: Trafficking protein particle complex subunit 5

MacromoleculeName: Trafficking protein particle complex subunit 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 22.371812 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: 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

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Macromolecule #7: TRAPPC2L

MacromoleculeName: TRAPPC2L / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 15.511826 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString:
MAFCIAVIGK DNAPLYLTTS DMEQELELQY HVNAALDVVE EKCLIGKGAP ESKELYLGLL YSTENHKIYG FVTNTRVKFI VVIDSSNVA LRENEVRAIF RNLHLLYTDA ICNPFYIPGE SLTSKKFDRA VQKLMSGTA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
50.0 mMHepes-KOH
250.0 mMKAc
1.0 mMDTT
0.005 (v/v)%Igepal C-630
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.2 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Details32% of the images were acquiring tilted the stage 19 degrees.
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1601314
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 353400
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 214.4
Output model

PDB-7b6d:
Drosophila melanogaster TRAPPCore (C1, C2, C2L, C3a/b, C4, C5, C6 subunits)

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