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- PDB-3cue: Crystal structure of a TRAPP subassembly activating the Rab Ypt1p -

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Basic information

Entry
Database: PDB / ID: 3cue
TitleCrystal structure of a TRAPP subassembly activating the Rab Ypt1p
Components
  • (Transport protein particle ...) x 4
  • GTP-binding protein YPT1
KeywordsPROTEIN TRANSPORT / membrane traffic / GEF / tethering complex / Rab activation / guanine nucleotide exchange factor / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Transport / Lipoprotein / Palmitate / GTP-binding / Nucleotide-binding / Phosphoprotein / Prenylation
Function / homology
Function and homology information


pre-mRNA catabolic process / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / TRAPPI protein complex / RAB geranylgeranylation / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex ...pre-mRNA catabolic process / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / TRAPPI protein complex / RAB geranylgeranylation / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / COPII-coated vesicle budding / cis-Golgi network membrane / cytoplasm to vacuole targeting by the Cvt pathway / protein localization to phagophore assembly site / intra-Golgi vesicle-mediated transport / phagophore assembly site membrane / Golgi stack / cis-Golgi network / endocytic recycling / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phagophore assembly site / retrograde transport, endosome to Golgi / cellular response to nitrogen starvation / reticulophagy / SNARE complex assembly / autophagosome assembly / chromosome organization / endoplasmic reticulum to Golgi vesicle-mediated transport / Neutrophil degranulation / endomembrane system / SNARE binding / intracellular protein transport / macroautophagy / cytoplasmic vesicle / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum / mitochondrion / cytosol
Similarity search - Function
Beta-Lactamase - #70 / Trafficking protein particle complex subunit 3 / Trafficking protein particle complex subunit / Sybindin-like family / Sybindin-like family / TRAPP I complex, subunit 5 / Bet3 family / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / : ...Beta-Lactamase - #70 / Trafficking protein particle complex subunit 3 / Trafficking protein particle complex subunit / Sybindin-like family / Sybindin-like family / TRAPP I complex, subunit 5 / Bet3 family / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / : / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / NO signalling/Golgi transport ligand-binding domain superfamily / Longin-like domain superfamily / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Beta-Lactamase / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / GTP-binding protein YPT1 / Trafficking protein particle complex subunit BET3 / Trafficking protein particle complex subunit 31 / Trafficking protein particle complex subunit BET5 / Trafficking protein particle complex subunit 23
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.7 Å
AuthorsCai, Y. / Reinisch, K.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes.
Authors: Cai, Y. / Chin, H.F. / Lazarova, D. / Menon, S. / Fu, C. / Cai, H. / Sclafani, A. / Rodgers, D.W. / De La Cruz, E.M. / Ferro-Novick, S. / Reinisch, K.M.
History
DepositionApr 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transport protein particle 23 kDa subunit
B: Transport protein particle 31 kDa subunit
C: Transport protein particle 18 kDa subunit
D: Transport protein particle 22 kDa subunit
E: Transport protein particle 22 kDa subunit
F: GTP-binding protein YPT1
G: Transport protein particle 23 kDa subunit
H: Transport protein particle 31 kDa subunit
I: Transport protein particle 18 kDa subunit
J: Transport protein particle 22 kDa subunit
K: Transport protein particle 22 kDa subunit
L: GTP-binding protein YPT1
M: Transport protein particle 23 kDa subunit
N: Transport protein particle 31 kDa subunit
O: Transport protein particle 18 kDa subunit
P: Transport protein particle 22 kDa subunit
Q: Transport protein particle 22 kDa subunit
R: GTP-binding protein YPT1
S: Transport protein particle 23 kDa subunit
T: Transport protein particle 31 kDa subunit
U: Transport protein particle 18 kDa subunit
V: Transport protein particle 22 kDa subunit
W: Transport protein particle 22 kDa subunit
X: GTP-binding protein YPT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)571,60128
Polymers570,57624
Non-polymers1,0264
Water00
1
A: Transport protein particle 23 kDa subunit
B: Transport protein particle 31 kDa subunit
C: Transport protein particle 18 kDa subunit
D: Transport protein particle 22 kDa subunit
E: Transport protein particle 22 kDa subunit
F: GTP-binding protein YPT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,9007
Polymers142,6446
Non-polymers2561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14980 Å2
ΔGint-82 kcal/mol
Surface area46490 Å2
MethodPISA
2
G: Transport protein particle 23 kDa subunit
H: Transport protein particle 31 kDa subunit
I: Transport protein particle 18 kDa subunit
J: Transport protein particle 22 kDa subunit
K: Transport protein particle 22 kDa subunit
L: GTP-binding protein YPT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,9007
Polymers142,6446
Non-polymers2561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15010 Å2
ΔGint-81.9 kcal/mol
Surface area46640 Å2
MethodPISA
3
M: Transport protein particle 23 kDa subunit
N: Transport protein particle 31 kDa subunit
O: Transport protein particle 18 kDa subunit
P: Transport protein particle 22 kDa subunit
Q: Transport protein particle 22 kDa subunit
R: GTP-binding protein YPT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,9007
Polymers142,6446
Non-polymers2561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15020 Å2
ΔGint-82.3 kcal/mol
Surface area46660 Å2
MethodPISA
4
S: Transport protein particle 23 kDa subunit
T: Transport protein particle 31 kDa subunit
U: Transport protein particle 18 kDa subunit
V: Transport protein particle 22 kDa subunit
W: Transport protein particle 22 kDa subunit
X: GTP-binding protein YPT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,9007
Polymers142,6446
Non-polymers2561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-82.1 kcal/mol
Surface area46690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.120, 115.400, 290.070
Angle α, β, γ (deg.)90.00, 90.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Transport protein particle ... , 4 types, 20 molecules AGMSBHNTCIOUDEJKPQVW

#1: Protein
Transport protein particle 23 kDa subunit / TRAPP 23 kDa subunit


Mass: 24889.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TRS23 / Plasmid: pETDuet-1, pCOLADuet-1, pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q03784
#2: Protein
Transport protein particle 31 kDa subunit / TRAPP 31 kDa subunit


Mass: 31755.689 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TRS31 / Plasmid: pETDuet-1, pCOLADuet-1, pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q03337
#3: Protein
Transport protein particle 18 kDa subunit / TRAPP 18 kDa subunit


Mass: 18453.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BET5 / Plasmid: pETDuet-1, pCOLADuet-1, pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q03630
#4: Protein
Transport protein particle 22 kDa subunit / TRAPP 22 kDa subunit


Mass: 22152.445 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BET3 / Plasmid: pETDuet-1, pCOLADuet-1, pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P36149

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Protein / Non-polymers , 2 types, 8 molecules FLRX

#5: Protein
GTP-binding protein YPT1 / TRAPP 22 kDa subunit


Mass: 23240.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YPT1, YP2 / Plasmid: pETDuet-1, pCOLADuet-1, pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P01123
#6: Chemical
ChemComp-PLM / PALMITIC ACID / Rab GTPase YPT1 / Transport GTPase YPT1 / Protein YP2


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3-5% PEG 20,000, 0.1 M MES, 3% (w/v) sorbitol, 5 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795, 0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2007
RadiationMonochromator: single crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.95371
ReflectionResolution: 3.7→50 Å / Num. all: 81195 / Num. obs: 81195 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 11.6
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7251 / Rsym value: 0.368 / % possible all: 91.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.7→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 5561 -7% set aside by the thin shell method
Rwork0.265 ---
all0.269 81195 --
obs0.265 81195 98.5 %-
Refinement stepCycle: LAST / Resolution: 3.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32708 0 68 0 32776
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.84
LS refinement shellResolution: 3.7→3.72 Å /
RfactorNum. reflection
Rfree0 0
Rwork0.383 -
obs-1472

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