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- PDB-3hie: Structure of the membrane-binding domain of the Sec3 subunit of t... -

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Basic information

Entry
Database: PDB / ID: 3hie
TitleStructure of the membrane-binding domain of the Sec3 subunit of the Exocyst complex
ComponentsExocyst complex component SEC3Exocyst
KeywordsEXOCYTOSIS / PH domain / dimer / domain swapping / phosphate-binding / Coiled coil / Phosphoprotein / Protein transport / Transport / LIPID BINDING PROTEIN
Function / homology
Function and homology information


exocyst assembly / Insulin processing / vesicle tethering involved in exocytosis / exocyst localization / endoplasmic reticulum inheritance / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport ...exocyst assembly / Insulin processing / vesicle tethering involved in exocytosis / exocyst localization / endoplasmic reticulum inheritance / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck / mating projection tip / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / small GTPase binding / protein transport / plasma membrane / cytoplasm
Similarity search - Function
PH-domain like - #90 / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Sec3 / Exocyst complex component Sec3, PIP2-binding N-terminal domain / Exocyst complex component Sec3, C-terminal / Exocyst complex component SEC3 N-terminal PIP2 binding PH / PH-domain like / Roll / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Exocyst complex component SEC3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsBaek, K. / Dominguez, R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure-function study of the N-terminal domain of exocyst subunit Sec3.
Authors: Baek, K. / Knodler, A. / Lee, S.H. / Zhang, X. / Orlando, K. / Zhang, J. / Foskett, T.J. / Guo, W. / Dominguez, R.
History
DepositionMay 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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: Exocyst complex component SEC3
C: Exocyst complex component SEC3
D: Exocyst complex component SEC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5256
Polymers80,3354
Non-polymers1902
Water4,486249
1
A: Exocyst complex component SEC3
B: Exocyst complex component SEC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3574
Polymers40,1672
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-38 kcal/mol
Surface area17390 Å2
MethodPISA
2
C: Exocyst complex component SEC3
D: Exocyst complex component SEC3


Theoretical massNumber of molelcules
Total (without water)40,1672
Polymers40,1672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-26 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.697, 68.486, 68.036
Angle α, β, γ (deg.)89.90, 82.17, 71.79
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 20083.654 Da / Num. of mol.: 4 / Fragment: UNP residues 71-241, Membrane-binding domain
Source method: isolated from a genetically manipulated source
Details: glutathione-S-transferase (GST) fusion
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: SEC3, PSL1, YER008C / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33332
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 0.1M Bicine, pH9.5, 14% PEG 5000 MME, 1mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 17-BM11
SYNCHROTRONAPS 17-BM20.9796
SYNCHROTRONAPS 17-BM30.9798
SYNCHROTRONAPS 17-BM40.974
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDOct 20, 2008
MAR CCD 165 mm2CCDOct 20, 2008
MAR CCD 165 mm3CCDOct 20, 2008
MAR CCD 165 mm4CCDOct 20, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
3MADMx-ray1
4MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.97981
40.9741
ReflectionResolution: 2→50 Å / Num. all: 46605 / Num. obs: 43622 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.053 / Net I/σ(I): 24.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.52 / % possible all: 62.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→38.74 Å / SU ML: 0.35 / Isotropic thermal model: Anisotropic / σ(F): 1.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 2203 5.05 %
Rwork0.202 --
obs0.204 43585 93.5 %
all-43624 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.13 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4722 Å20.6602 Å2-0.9418 Å2
2--1.3535 Å2-0.6486 Å2
3---1.1187 Å2
Refinement stepCycle: LAST / Resolution: 2→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5357 0 10 249 5616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.025
X-RAY DIFFRACTIONf_angle_d
X-RAY DIFFRACTIONf_dihedral_angle_d21.689
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04360.3737810.32981432X-RAY DIFFRACTION52
2.0436-2.09110.35481190.30382180X-RAY DIFFRACTION79
2.0911-2.14340.31021440.28952521X-RAY DIFFRACTION90
2.1434-2.20130.32551400.27892555X-RAY DIFFRACTION94
2.2013-2.26610.28651420.2672706X-RAY DIFFRACTION97
2.2661-2.33920.30761560.2672647X-RAY DIFFRACTION98
2.3392-2.42280.31761360.26342727X-RAY DIFFRACTION98
2.4228-2.51980.32181490.2632702X-RAY DIFFRACTION98
2.5198-2.63450.31511490.25632713X-RAY DIFFRACTION98
2.6345-2.77330.2971420.24392711X-RAY DIFFRACTION98
2.7733-2.9470.28631310.23152763X-RAY DIFFRACTION98
2.947-3.17450.27851450.2242718X-RAY DIFFRACTION99
3.1745-3.49380.25331460.18972727X-RAY DIFFRACTION99
3.4938-3.99890.21491380.16992779X-RAY DIFFRACTION99
3.9989-5.03640.16761480.13892726X-RAY DIFFRACTION99
5.0364-38.74880.20241370.16572775X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
1refined-0.36180.7075-0.86931.1256-0.68524.5878-0.0718-0.17670.6238-0.0938-0.2956-0.47870.0293-0.18670.19080.1111-0.03910.0040.17480.03160.2548-2.3036-12.019214.4202
22.0578-0.0613-0.20581.8749-0.09591.5253-0.0034-0.12330.4850.1212-0.0051-0.1182-0.18030.0232-0.14090.029-0.0313-0.00790.0246-0.03680.1189
3-0.72980.07560.57844.1327-0.65131.35450.079-0.0040.64110.0077-0.111-0.81170.0040.25520.17240.0734-0.0266-0.03640.09890.03860.2207
41.7052-1.72390.88116.24970.98881.0880.1632-0.50830.3374-0.0616-0.2399-0.7542-0.13380.2805-0.05980.0706-0.0029-0.01080.08590.02240.1923
51.89240.1765-0.11662.25840.06581.24790.041-0.12670.09530.02040.0065-0.10990.0718-0.0953-0.02330.05060.00030.01430.0337-0.00320.0554
60.24020.22030.03372.22720.31980.3133-0.0352-0.1216-0.15410.2441-0.0092-0.4191-0.2273-0.21210.18330.297-0.02790.00530.09860.03730.1269
72.4894-0.51830.41481.8021-1.06110.9750.7647-0.4394-0.5972-0.0254-0.4265-0.04870.26310.1063-0.16570.5467-0.1032-0.00690.19810.010.1471
82.045-0.86410.19681.14290.53771.4236-0.11580.4818-0.1852-0.2339-0.27330.03850.51450.05810.17770.3191-0.09390.01280.1401-0.0260.1193
94.60172.37091.1958-0.23670.48810.629-0.2482-0.1749-0.3317-0.0599-0.006-0.35140.509-0.05950.19270.2888-0.01990.07430.029-0.05080.2514
100.9496-0.23310.14250.39040.7990.72380.09190.0856-0.8308-0.1391-0.0291-0.96460.6320.06020.18250.421-0.08560.01510.1126-0.03670.281
111.15480.26510.63382.99990.73371.64610.08070.00050.0815-0.2611-0.1608-0.09710.1388-0.17590.08480.1879-0.01260.03190.0747-0.02310.0466
12-0.72121.57350.20462.3162.04420.22130.21030.1513-0.1436-0.0869-0.1177-0.1008-0.1858-0.2147-0.05180.14570.00630.04480.138-0.00260.1681
130.7215-0.74563.84551.0863-0.03695.20850.0845-0.20130.1124-0.29370.00040.3398-0.86990.36220.07820.63710.02050.19320.7177-0.03150.6989
14-0.02130.3197-0.29880.7399-1.47081.15450.20360.1320.1488-0.0135-0.08380.1571-0.27260.03610.05010.27540.0234-0.02590.22870.02560.2906
153.19411.41030.77461.1082-0.13540.64360.1387-0.0120.6368-0.0897-0.13880.0883-0.3393-0.1698-0.05720.3561-0.0097-0.09150.20630.13360.2649
161.08180.81120.5221.7048-0.34690.9751-0.00130.31910.5972-1.27460.34340.48770.0159-0.1178-0.06870.30550.0195-0.11230.27260.12490.2959
171.24640.0246-0.17072.7421-1.05950.8556-0.00850.09460.14610.0396-0.1062-0.0859-0.08950.11480.09250.2509-0.0473-0.02960.21320.00630.0691
181.11610.56431.50730.361-1.3367-1.08810.6166-0.1749-0.9694-0.03930.54140.05092.11780.5068-0.22090.9973-0.2544-0.11950.7694-0.12060.6475
190.83481.0281-1.54120.7909-0.27891.5237-0.23420.1373-0.2023-0.06030.30270.2970.2725-0.30660.00430.1848-0.0791-0.02710.22920.06880.2055
200.14190.3280.50491.2235-1.16583.1790.0035-0.03830.00420.1360.1490.1958-0.137-0.2802-0.13410.13640.02070.06890.17470.02030.1112
Refinement TLS groupSelection details: CHAIN D AND RESI 161:241

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