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- PDB-1h8m: Solution structure of ykt6 -

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Basic information

Entry
Database: PDB / ID: 1h8m
TitleSolution structure of ykt6
ComponentsSYNAPTOBREVIN HOMOLOG 1
KeywordsENDOCYTOSIS/EXOCYTOSIS / TRANSMEMBRANE LIPOPROTEIN / PRENYLATION / ENDOCYTOSIS-EXOCYTOSIS complex
Function / homology
Function and homology information


amphisome-lysosome fusion / Golgi cis cisterna membrane / Golgi vesicle fusion to target membrane / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / vacuole fusion, non-autophagic / COPI-mediated anterograde transport / Golgi to endosome transport / COPII-mediated vesicle transport / palmitoyltransferase activity ...amphisome-lysosome fusion / Golgi cis cisterna membrane / Golgi vesicle fusion to target membrane / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / vacuole fusion, non-autophagic / COPI-mediated anterograde transport / Golgi to endosome transport / COPII-mediated vesicle transport / palmitoyltransferase activity / vesicle fusion / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / fungal-type vacuole / vacuolar membrane / autophagosome membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / intracellular protein transport / endosome membrane / endosome / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
YKT6, SNARE motif / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain ...YKT6, SNARE motif / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Synaptobrevin homolog YKT6
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR
Model type detailsMINIMIZED AVERAGE
AuthorsTochio, H. / Tsui, M.M.K. / Banfield, D.K. / Zhang, M.
CitationJournal: Science / Year: 2001
Title: An Autoinhibitory Mechanism for Nonsyntaxin Snare Proteins Revealed by the Structure of Ykt6P
Authors: Tochio, H. / Tsui, M.M.K. / Banfield, D.K. / Zhang, M.
History
DepositionFeb 10, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SYNAPTOBREVIN HOMOLOG 1


Theoretical massNumber of molelcules
Total (without water)15,8551
Polymers15,8551
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)1 / -
Representative

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Components

#1: Protein SYNAPTOBREVIN HOMOLOG 1


Mass: 15854.735 Da / Num. of mol.: 1 / Fragment: N-TERMINAL / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P36015

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 7.0 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: 1
Developer: BRUNGER STRUCTURAL STATISTICS: RMSD SD NOE DISTANCE RESTRAINTS (2350) 0.025 A 0.001 A DIHEDRAL ANGLE RESTRAINTS (157) 0.584 DEG 0.036 DEG BONDS 0.003 A 0.000 A ANGLES 0.435 DEG 0.012 DEG ...Developer: BRUNGER STRUCTURAL STATISTICS: RMSD SD NOE DISTANCE RESTRAINTS (2350) 0.025 A 0.001 A DIHEDRAL ANGLE RESTRAINTS (157) 0.584 DEG 0.036 DEG BONDS 0.003 A 0.000 A ANGLES 0.435 DEG 0.012 DEG IMPROPERS 0.336 DEG 0.014 DEG DIHEDRALS 29.969 DEG 0.887 DEG ENOE -30.74 40.95 ECDIH 3.28 0.40 EBOND 14.68 1.25 EANGLE 115.61 6.40 EI
Classification: refinement
NMR ensembleConformers submitted total number: 1

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