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- PDB-2eqb: Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, ... -

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Basic information

Entry
Database: PDB / ID: 2eqb
TitleCrystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex
Components
  • Rab guanine nucleotide exchange factor SEC2
  • Ras-related protein SEC4
KeywordsENDOCYTOSIS/EXOCYTOSIS / coiled coil / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


ascospore-type prospore assembly / Golgi to plasma membrane transport vesicle / Anchoring of the basal body to the plasma membrane / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / cell tip / incipient cellular bud site / vesicle fusion / cellular bud tip ...ascospore-type prospore assembly / Golgi to plasma membrane transport vesicle / Anchoring of the basal body to the plasma membrane / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / cell tip / incipient cellular bud site / vesicle fusion / cellular bud tip / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck / regulation of exocytosis / mating projection tip / phosphatidylinositol-4-phosphate binding / transport vesicle membrane / exocytosis / protein secretion / transport vesicle / Neutrophil degranulation / guanyl-nucleotide exchange factor activity / protein localization to plasma membrane / autophagy / protein transport / vesicle / mitochondrial outer membrane / endosome / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4880 / GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4880 / GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ras-related protein SEC4 / Rab guanine nucleotide exchange factor SEC2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsSato, Y. / Fukai, S. / Ishitani, R. / Nureki, O.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structure of the Sec4p{middle dot}Sec2p complex in the nucleotide exchanging intermediate state
Authors: Sato, Y. / Fukai, S. / Ishitani, R. / Nureki, O.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Ras-related protein SEC4
B: Rab guanine nucleotide exchange factor SEC2
C: Rab guanine nucleotide exchange factor SEC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4205
Polymers42,2303
Non-polymers1902
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-67 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.581, 117.422, 123.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ras-related protein SEC4 / Suppressor of RHO3 protein 6 / Rab GTPase Sec4p


Mass: 19447.211 Da / Num. of mol.: 1 / Fragment: residues 19-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P07560
#2: Protein Rab guanine nucleotide exchange factor SEC2 / GDP-GTP exchange factor SEC2


Mass: 11391.563 Da / Num. of mol.: 2 / Fragment: GEF domain, residues 51-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P17065
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5 Å3/Da / Density % sol: 75.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 150mM Dipotassium hydrogenphosphate, 17% PEG 3350, 150mM dimethyl(2-hydroxyethyl)ammonium propane sulfonate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONPhoton Factory BL-5A20.97956, 0.97973
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 12, 2006
ADSC QUANTUM 3152CCDDec 21, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979561
30.979731
ReflectionResolution: 2.7→50 Å / Num. all: 23619 / Num. obs: 23619 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.6 Å2 / Net I/σ(I): 12.7
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 2.07 / Rsym value: 0.288

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→48.08 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3233822.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1121 4.8 %RANDOM
Rwork0.273 ---
obs0.273 23220 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.4236 Å2 / ksol: 0.307169 e/Å3
Displacement parametersBiso mean: 77.7 Å2
Baniso -1Baniso -2Baniso -3
1--20.9 Å20 Å20 Å2
2--40.93 Å20 Å2
3----20.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.9 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 10 114 3023
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.831.5
X-RAY DIFFRACTIONc_mcangle_it4.922
X-RAY DIFFRACTIONc_scbond_it3.652
X-RAY DIFFRACTIONc_scangle_it5.912.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.433 178 4.8 %
Rwork0.441 3559 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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