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- PDB-3a58: Crystal structure of Sec3p - Rho1p complex from Saccharomyces cer... -

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Basic information

Entry
Database: PDB / ID: 3a58
TitleCrystal structure of Sec3p - Rho1p complex from Saccharomyces cerevisiae
Components
  • Exocyst complex component SEC3Exocyst
  • GTP-binding protein RHO1
KeywordsPROTEIN TRANSPORT/EXOCYTOSIS / protein complex / PH domain / GTPase / membrane traffic / Exocytosis / Phosphoprotein / Protein transport / Transport / Cell membrane / Endosome / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Peroxisome / Prenylation / PROTEIN TRANSPORT-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


regulation of cell wall (1->3)-beta-D-glucan biosynthetic process / regulation of secondary cell septum biogenesis / PI3K/AKT activation / G beta:gamma signalling through PI3Kgamma / RHO GTPases activate PKNs / : / cellular bud neck septin ring organization / G alpha (12/13) signalling events / regulation of exocyst localization / 1,3-beta-D-glucan synthase complex ...regulation of cell wall (1->3)-beta-D-glucan biosynthetic process / regulation of secondary cell septum biogenesis / PI3K/AKT activation / G beta:gamma signalling through PI3Kgamma / RHO GTPases activate PKNs / : / cellular bud neck septin ring organization / G alpha (12/13) signalling events / regulation of exocyst localization / 1,3-beta-D-glucan synthase complex / positive regulation of mitotic actomyosin contractile ring assembly / exocyst assembly / budding cell bud growth / exocyst localization / regulation of fungal-type cell wall organization / Insulin processing / endoplasmic reticulum inheritance / : / exocyst / cellular bud / regulation of vacuole fusion, non-autophagic / prospore membrane / positive regulation of protein kinase C signaling / incipient cellular bud site / cellular bud tip / cortical cytoskeleton organization / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck / mating projection tip / fungal-type vacuole membrane / peroxisomal membrane / regulation of cell size / small GTPase-mediated signal transduction / positive regulation of endocytosis / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / cell projection / actin filament organization / cell periphery / regulation of actin cytoskeleton organization / small GTPase binding / peroxisome / G-protein beta-subunit binding / regulation of protein localization / protein transport / cell cortex / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / mitochondrial outer membrane / cytoskeleton / endosome membrane / intracellular membrane-bounded organelle / GTPase activity / GTP binding / protein kinase binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / plasma membrane / cytoplasm
Similarity search - Function
PH-domain like - #90 / Exocyst complex component Sec3, C-terminal / Exocyst complex component Sec3, PIP2-binding N-terminal domain / : / Exocyst complex component Sec3, coiled-coil / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Sec3, C-terminal / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Small GTPase Rho / small GTPase Rho family profile. ...PH-domain like - #90 / Exocyst complex component Sec3, C-terminal / Exocyst complex component Sec3, PIP2-binding N-terminal domain / : / Exocyst complex component Sec3, coiled-coil / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Sec3, C-terminal / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Small GTPase Rho / small GTPase Rho family profile. / PH-domain like / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / PHOSPHATE ION / GTP-binding protein RHO1 / Exocyst complex component SEC3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsYamashita, M. / Sato, Y. / Yamagata, A. / Mimura, H. / Yoshikawa, A. / Fukai, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis for the Rho- and phosphoinositide-dependent localization of the exocyst subunit Sec3
Authors: Yamashita, M. / Kurokawa, K. / Sato, Y. / Yamagata, A. / Mimura, H. / Yoshikawa, A. / Sato, K. / Nakano, A. / Fukai, S.
History
DepositionAug 3, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Exocyst complex component SEC3
B: GTP-binding protein RHO1
C: Exocyst complex component SEC3
D: GTP-binding protein RHO1
E: Exocyst complex component SEC3
F: GTP-binding protein RHO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,40419
Polymers171,1006
Non-polymers2,30413
Water1,76598
1
A: Exocyst complex component SEC3
B: GTP-binding protein RHO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8657
Polymers57,0332
Non-polymers8315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-36 kcal/mol
Surface area18680 Å2
MethodPISA
2
C: Exocyst complex component SEC3
D: GTP-binding protein RHO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8657
Polymers57,0332
Non-polymers8315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-37 kcal/mol
Surface area18050 Å2
MethodPISA
3
E: Exocyst complex component SEC3
F: GTP-binding protein RHO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6755
Polymers57,0332
Non-polymers6413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-27 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.000, 116.054, 247.675
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Exocyst complex component SEC3 / Exocyst / Sec3p / Protein PSL1


Mass: 36266.977 Da / Num. of mol.: 3 / Fragment: residues 1-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC3, PSL1, YER008C / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P33332
#2: Protein GTP-binding protein RHO1 / Rho1p / Rho-type GTPase 1


Mass: 20766.385 Da / Num. of mol.: 3 / Fragment: residues 1-188 / Mutation: F30N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RHO1, YPR165W, P9325.3 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P06780

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Non-polymers , 4 types, 111 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM HEPES-Na (pH6.5), 100mM NaCl, 1.4M ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 52847 / Num. obs: 52847 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 12.9
Reflection shellResolution: 2.6→2.64 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.44 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→47.85 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 249257.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2662 5 %RANDOM
Rwork0.234 50076 --
obs0.235 52738 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.93 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 147.93 Å2 / Biso mean: 70.578 Å2 / Biso min: 22.72 Å2
Baniso -1Baniso -2Baniso -3
1--5.751 Å20 Å20 Å2
2---5.756 Å20 Å2
3---11.507 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8560 0 134 98 8792
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_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4411.5
X-RAY DIFFRACTIONc_scbond_it1.8752
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scangle_it2.9892.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 455 5.3 %
Rwork0.327 8195 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3gnp.paramgnp.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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