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- EMDB-12063: Whole MiniTRAPPIII -

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Basic information

Entry
Database: EMDB / ID: EMD-12063
TitleWhole MiniTRAPPIII
Map data
Sample
  • Complex: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific subunits
    • 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
    • Protein or peptide: FI18195p1
    • Protein or peptide: Trafficking protein particle complex subunit 11
KeywordsRab1 / GEFs / Golgi / TRAPP complexes / 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 / cis-Golgi network membrane / Golgi vesicle transport / Neutrophil degranulation / cis-Golgi network ...COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / cis-Golgi network membrane / Golgi vesicle transport / Neutrophil degranulation / cis-Golgi network / intra-Golgi vesicle-mediated transport / protein secretion / long-term memory / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular transport / vesicle-mediated transport / trans-Golgi network / spermatogenesis / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / nucleus / cytoplasm / cytosol
Similarity search - Function
Trafficking protein particle complex subunit 2-like / : / Trafficking protein particle complex subunit 11 / Trafficking protein particle complex subunit 11, C-terminal / Foie gras liver health family 1 / Gryzun, putative Golgi trafficking / TRAPP III complex, Trs85 / ER-Golgi trafficking TRAPP I complex 85 kDa subunit / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region ...Trafficking protein particle complex subunit 2-like / : / Trafficking protein particle complex subunit 11 / Trafficking protein particle complex subunit 11, C-terminal / Foie gras liver health family 1 / Gryzun, putative Golgi trafficking / TRAPP III complex, Trs85 / ER-Golgi trafficking TRAPP I complex 85 kDa subunit / 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 11 / Trafficking protein particle complex subunit / Trafficking protein particle complex subunit 6B / Trafficking protein particle complex subunit / Trafficking protein particle complex subunit / Probable trafficking protein particle complex subunit 2 / FI18195p1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsGalindo A / Munro S
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 9, 2020-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b70
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12063.png

Downloads & links

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Map

FileDownload / File: emd_12063.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.2564 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.009
Minimum - Maximum-0.014434552 - 0.05975762
Average (Standard dev.)0.000024555075 (±0.0016248442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 502.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.25641.25641.2564
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z502.560502.560502.560
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-0.0140.0600.000

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Supplemental data

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Mask #1

Fileemd_12063_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific s...

EntireName: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific subunits
Components
  • Complex: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific subunits
    • 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
    • Protein or peptide: FI18195p1
    • Protein or peptide: Trafficking protein particle complex subunit 11

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Supramolecule #1: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific s...

SupramoleculeName: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific subunits
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 453 KDa

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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: 20.492309 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 LEEVIPAGED

UniProtKB: Trafficking protein particle complex subunit

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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

UniProtKB: Trafficking protein particle complex subunit 6B

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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

UniProtKB: Trafficking protein particle complex subunit

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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

UniProtKB: Trafficking protein particle complex subunit

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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

UniProtKB: Probable trafficking protein particle complex subunit 2

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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

UniProtKB: Trafficking protein particle complex subunit 5

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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

UniProtKB: Trafficking protein particle complex subunit 2-like protein

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Macromolecule #8: FI18195p1

MacromoleculeName: FI18195p1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 28.378545 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: DNLRHFVQDY AVRALIPYIE HLVAILAEGV TNKKGVSKSL LSATKRWFVT SKPGAGANNQ NAVIYTNESA ELQTRKLGDL YFMFGHYNL AFQSYHQAKR DFNADSAWQY YAGALEMAAL SAFMLGTAQR KTYDYMEDAI VCYLTVCKLQ QFATRATLLS M ECLKTARL ...String:
DNLRHFVQDY AVRALIPYIE HLVAILAEGV TNKKGVSKSL LSATKRWFVT SKPGAGANNQ NAVIYTNESA ELQTRKLGDL YFMFGHYNL AFQSYHQAKR DFNADSAWQY YAGALEMAAL SAFMLGTAQR KTYDYMEDAI VCYLTVCKLQ QFATRATLLS M ECLKTARL YSEVAKQLIR MTNEESDLRS ALLLEQAAYC FLVTQPPMHR KYAFHIVLAG NRYSRAGQRK HAYRCYRQAY QV FQKREW

UniProtKB: FI18195p1

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Macromolecule #9: Trafficking protein particle complex subunit 11

MacromoleculeName: Trafficking protein particle complex subunit 11 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 81.847164 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: 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

UniProtKB: Trafficking protein particle complex subunit 11

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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

Concentration0.5 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 - Time: 45 sec. / 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3443 / Average exposure time: 0.3 sec. / Average electron dose: 45.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen 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

Particle selectionNumber selected: 1242082
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 486758
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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