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- PDB-2b7m: Crystal Structure of the S. cerevisiae Exocyst Component Exo70p -

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Basic information

Entry
Database: PDB / ID: 2b7m
TitleCrystal Structure of the S. cerevisiae Exocyst Component Exo70p
ComponentsExocyst complex component EXO70
KeywordsENDOCYTOSIS/EXOCYTOSIS / exocyst / exocytosis / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


exocyst assembly / exocyst localization / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / cellular bud neck / Golgi to plasma membrane transport / mating projection tip / vesicle docking involved in exocytosis ...exocyst assembly / exocyst localization / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / cellular bud neck / Golgi to plasma membrane transport / mating projection tip / vesicle docking involved in exocytosis / exocytosis / transport vesicle / Rho protein signal transduction / phosphatidylinositol-4,5-bisphosphate binding / small GTPase binding / protein transport / plasma membrane / cytoplasm
Similarity search - Function
Exocyst complex component Exo70 / Exocyst complex component Exo70 / Exocyst complex subunit Exo70, C-terminal / Exo70 exocyst complex subunit C-terminal / Exocyst complex component Exo70 N-terminal / Cullin repeat-like-containing domain superfamily / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Exocyst complex component EXO70
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å
AuthorsHamburger, Z.A. / Hamburger, A.E. / West, A.P. / Weis, W.I.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the S.cerevisiae Exocyst Component Exo70p
Authors: Hamburger, Z.A. / Hamburger, A.E. / West, A.P. / Weis, W.I.
History
DepositionOct 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 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_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: Exocyst complex component EXO70
B: Exocyst complex component EXO70
C: Exocyst complex component EXO70
D: Exocyst complex component EXO70


Theoretical massNumber of molelcules
Total (without water)262,1504
Polymers262,1504
Non-polymers00
Water00
1
A: Exocyst complex component EXO70


Theoretical massNumber of molelcules
Total (without water)65,5371
Polymers65,5371
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exocyst complex component EXO70


Theoretical massNumber of molelcules
Total (without water)65,5371
Polymers65,5371
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Exocyst complex component EXO70


Theoretical massNumber of molelcules
Total (without water)65,5371
Polymers65,5371
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Exocyst complex component EXO70


Theoretical massNumber of molelcules
Total (without water)65,5371
Polymers65,5371
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)415.729, 55.129, 132.930
Angle α, β, γ (deg.)90.00, 104.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Exocyst complex component EXO70 / Exocyst complex protein of 70 kDa


Mass: 65537.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EXO70 / Plasmid: pProEx-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): RIL+ / References: UniProt: P19658
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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.1 M MES pH 6.1, 20 % PEG 20000, 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97950, 0.97963, 0.9393
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 5, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979631
30.93931
ReflectionResolution: 3.5→20 Å / Num. all: 36080 / Num. obs: 36080 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.076 / Net I/σ(I): 12.6
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 3 % / Rsym value: 0.354 / % possible all: 92

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.5→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4031626.48 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 2175 6.1 %SHELLS
Rwork0.254 ---
obs0.254 35904 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.2292 Å2 / ksol: 0.157954 e/Å3
Displacement parametersBiso mean: 129.2 Å2
Baniso -1Baniso -2Baniso -3
1--11.77 Å20 Å240.72 Å2
2--15.15 Å20 Å2
3----3.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16823 0 0 0 16823
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.62 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.436 229 6.4 %
Rwork0.349 3356 -
obs--96.9 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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