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- PDB-2e7s: Crystal structure of the yeast Sec2p GEF domain -

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Basic information

Entry
Database: PDB / ID: 2e7s
TitleCrystal structure of the yeast Sec2p GEF domain
ComponentsRab guanine nucleotide exchange factor SEC2
KeywordsENDOCYTOSIS/EXOCYTOSIS / COILED COIL / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


Golgi to plasma membrane transport vesicle / Anchoring of the basal body to the plasma membrane / RAB GEFs exchange GTP for GDP on RABs / cell tip / cellular bud tip / cellular bud neck / mating projection tip / phosphatidylinositol-4-phosphate binding / exocytosis / transport vesicle ...Golgi to plasma membrane transport vesicle / Anchoring of the basal body to the plasma membrane / RAB GEFs exchange GTP for GDP on RABs / cell tip / cellular bud tip / cellular bud neck / mating projection tip / phosphatidylinositol-4-phosphate binding / exocytosis / transport vesicle / guanyl-nucleotide exchange factor activity / autophagy / protein transport / identical protein binding / cytosol
Similarity search - Function
GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p
Similarity search - Domain/homology
Rab guanine nucleotide exchange factor SEC2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsFukai, S. / Sato, Y. / Nureki, O.
CitationJournal: Structure / Year: 2007
Title: Asymmetric Coiled-Coil Structure with Guanine Nucleotide Exchange Activity
Authors: Sato, Y. / Shirakawa, R. / Horiuchi, H. / Dohmae, N. / Fukai, S. / Nureki, O.
History
DepositionJan 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rab guanine nucleotide exchange factor SEC2
B: Rab guanine nucleotide exchange factor SEC2
C: Rab guanine nucleotide exchange factor SEC2
D: Rab guanine nucleotide exchange factor SEC2
E: Rab guanine nucleotide exchange factor SEC2
F: Rab guanine nucleotide exchange factor SEC2
G: Rab guanine nucleotide exchange factor SEC2
H: Rab guanine nucleotide exchange factor SEC2
I: Rab guanine nucleotide exchange factor SEC2
J: Rab guanine nucleotide exchange factor SEC2
K: Rab guanine nucleotide exchange factor SEC2
L: Rab guanine nucleotide exchange factor SEC2
M: Rab guanine nucleotide exchange factor SEC2
N: Rab guanine nucleotide exchange factor SEC2
O: Rab guanine nucleotide exchange factor SEC2
P: Rab guanine nucleotide exchange factor SEC2
Q: Rab guanine nucleotide exchange factor SEC2
R: Rab guanine nucleotide exchange factor SEC2
S: Rab guanine nucleotide exchange factor SEC2
T: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)315,61020
Polymers315,61020
Non-polymers00
Water4,720262
1
A: Rab guanine nucleotide exchange factor SEC2
B: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-30 kcal/mol
Surface area19870 Å2
MethodPISA
2
C: Rab guanine nucleotide exchange factor SEC2
D: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-35 kcal/mol
Surface area20410 Å2
MethodPISA
3
E: Rab guanine nucleotide exchange factor SEC2
F: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-34 kcal/mol
Surface area20630 Å2
MethodPISA
4
G: Rab guanine nucleotide exchange factor SEC2
H: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-29 kcal/mol
Surface area18220 Å2
MethodPISA
5
I: Rab guanine nucleotide exchange factor SEC2
J: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-29 kcal/mol
Surface area18350 Å2
MethodPISA
6
K: Rab guanine nucleotide exchange factor SEC2
L: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-30 kcal/mol
Surface area19550 Å2
MethodPISA
7
M: Rab guanine nucleotide exchange factor SEC2
N: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-27 kcal/mol
Surface area19050 Å2
MethodPISA
8
O: Rab guanine nucleotide exchange factor SEC2
P: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-31 kcal/mol
Surface area19990 Å2
MethodPISA
9
Q: Rab guanine nucleotide exchange factor SEC2
R: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-26 kcal/mol
Surface area18490 Å2
MethodPISA
10
S: Rab guanine nucleotide exchange factor SEC2
T: Rab guanine nucleotide exchange factor SEC2


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-30 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.937, 176.569, 181.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Rab guanine nucleotide exchange factor SEC2 / GDP-GTP exchange factor SEC2


Mass: 15780.514 Da / Num. of mol.: 20 / Fragment: GEF DOMAIN, residues 31-160 / Mutation: M115L/K121M/T142M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P17065
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 1

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Sample preparation

CrystalDensity Matthews: 5.1736 Å3/Da / Density % sol: 76.2257 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM Tris, 10mM magnesium chloride, 3% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 25, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 65695 / Num. obs: 65695 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 29.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6357 / Rsym value: 0.422 / % possible all: 98.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (h, -k, -l) AND THE TWINNING FRACTION IS 0.500.
RfactorNum. reflectionSelection details
Rfree0.285 -RANDOM
Rwork0.229 --
all-65695 -
obs-65695 -
Displacement parametersBiso mean: 138.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å / Luzzati sigma a obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19008 0 0 262 19270
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_improper_angle_d0.61

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