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- PDB-2d2s: Crystal Structure of the Exo84p C-terminal Domains -

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Basic information

Entry
Database: PDB / ID: 2d2s
TitleCrystal Structure of the Exo84p C-terminal Domains
ComponentsExocyst complex component EXO84
KeywordsENDOCYTOSIS/EXOCYTOSIS / tethering complex / exocyst / Exo84p / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


exocyst assembly / exocyst localization / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / vesicle docking involved in exocytosis ...exocyst assembly / exocyst localization / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / vesicle docking involved in exocytosis / spliceosomal complex assembly / exocytosis / transport vesicle / protein localization / protein transport
Similarity search - Function
Exo84p, N-terminal helical domain / Exo84p, C-terminal helical domain / Exocyst component Exo84, C-terminal / Exocyst complex component Exo84 / Exocyst component Exo84, C-terminal, subdomain 2 / Exocyst component Exo84, C-terminal, subdomain 1 / Exocyst component 84 C-terminal / Vps51/EXO84/COG1 N-terminal / Cullin repeat-like-containing domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Exo84p, N-terminal helical domain / Exo84p, C-terminal helical domain / Exocyst component Exo84, C-terminal / Exocyst complex component Exo84 / Exocyst component Exo84, C-terminal, subdomain 2 / Exocyst component Exo84, C-terminal, subdomain 1 / Exocyst component 84 C-terminal / Vps51/EXO84/COG1 N-terminal / Cullin repeat-like-containing domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Exocyst complex component EXO84
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.85 Å
AuthorsDong, G. / Hutagalung, A.H. / Fu, C. / Novick, P. / Reinisch, K.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The structures of exocyst subunit Exo70p and the Exo84p C-terminal domains reveal a common motif
Authors: Dong, G. / Hutagalung, A.H. / Fu, C. / Novick, P. / Reinisch, K.M.
History
DepositionSep 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2005Provider: 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exocyst complex component EXO84


Theoretical massNumber of molelcules
Total (without water)26,8371
Polymers26,8371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.850, 54.850, 209.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Exocyst complex component EXO84 / Exocyst complex protein of 84 kDa / U1-SNP1 associating protein 3


Mass: 26836.611 Da / Num. of mol.: 1 / Fragment: Exo84p C-terminal domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38261

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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: 2.93 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3000, iso-propanol, sodium cloride, dithiothreitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.85→15 Å / Num. all: 13025 / Num. obs: 13025 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.85→2.95 Å / % possible all: 57.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.85→15 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.306 1101 RANDOM
Rwork0.269 --
all0.31 13025 -
obs0.273 12362 -
Refinement stepCycle: LAST / Resolution: 2.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 0 0 1742

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