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- PDB-1hk6: Ral binding domain from Sec5 -

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Basic information

Entry
Database: PDB / ID: 1hk6
TitleRal binding domain from Sec5
ComponentsEXOCYST COMPLEX COMPONENT SEC5Exocyst
KeywordsEXOCYTOSIS / IPT RAL SEC5 EXOCYST / PROTEIN TRANSPORT / IMMUNOGLOBULIN FOLD
Function / homology
Function and homology information


Insulin processing / small GTPase binding => GO:0031267 / VxPx cargo-targeting to cilium / regulation of entry of bacterium into host cell / exocyst / : / Golgi to plasma membrane transport / Flemming body / exocytosis / positive regulation of exocytosis ...Insulin processing / small GTPase binding => GO:0031267 / VxPx cargo-targeting to cilium / regulation of entry of bacterium into host cell / exocyst / : / Golgi to plasma membrane transport / Flemming body / exocytosis / positive regulation of exocytosis / vesicle-mediated transport / protein transport / protein kinase binding / plasma membrane
Similarity search - Function
Exocyst complex component EXOC2/Sec5 / Exocyst complex component EXOC2/Sec5, N-terminal domain / Exocyst complex component Sec5 / IPT/TIG domain / IPT domain / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Exocyst complex component 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsMott, H.R. / Nietlispach, D. / Hopkins, L.J. / Mirey, G. / Camonis, J.H. / Owen, D.
CitationJournal: J. Biol. Chem. / Year: 2003
Title: Structure of the GTPase-binding domain of Sec5 and elucidation of its Ral binding site.
Authors: Mott, H.R. / Nietlispach, D. / Hopkins, L.J. / Mirey, G. / Camonis, J.H. / Owen, D.
History
DepositionMar 5, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXOCYST COMPLEX COMPONENT SEC5


Theoretical massNumber of molelcules
Total (without water)10,1151
Polymers10,1151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein EXOCYST COMPLEX COMPONENT SEC5 / Exocyst / SEC5L1


Mass: 10114.772 Da / Num. of mol.: 1 / Fragment: IPT DOMAIN, RESIDUES 5-97
Source method: isolated from a genetically manipulated source
Details: HIS-MET AT N-TERMINUS FROM CLONING / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9D4H1
Compound detailsPART OF THE EXOCYST COMPLEX INVOLVED IN THE DOCKING OF EXOCYSTIC VESICLES WITH FUSION SITES ON THE ...PART OF THE EXOCYST COMPLEX INVOLVED IN THE DOCKING OF EXOCYSTIC VESICLES WITH FUSION SITES ON THE PLASMA MEMBRANE. THE EXOCYST COMPLEX IS COMPOSED OF VARIOUS SUBUNITS NAMED AS SEC3,SEC5,SEC6,SEC8,SEC10,SEC15,EXO70 AND EXO84.
Sequence detailsHIS A 3, INSERTION CLONING ARTEFACT MET A 4, INSERTION CLONING ARTEFACT

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
NMR detailsText: STRUCTURE WAS DETERMINED USING 15N-LEBELLED AND 13C,15N-LABELLED SEC5

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Sample preparation

Sample conditionsIonic strength: 200 mM / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGERrefinement
CNS/ARIA1.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL ABOVE
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 25

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