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- PDB-3kyq: Lipid-induced Conformational Switch Controls Fusion Activity of L... -

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Basic information

Entry
Database: PDB / ID: 3kyq
TitleLipid-induced Conformational Switch Controls Fusion Activity of Longin Domain SNARE Ykt6
ComponentsSynaptobrevin homolog YKT6
KeywordsTRANSFERASE / v-SNARE homolog / lipid binding / Cytoplasmic vesicle / ER-Golgi transport / Golgi apparatus / Lipoprotein / Palmitate / Prenylation / Protein transport / Transport
Function / homology
Function and homology information


Intra-Golgi traffic / protein-cysteine S-palmitoyltransferase activity / COPI-mediated anterograde transport / vesicle targeting / basal dendrite / COPII-mediated vesicle transport / SNARE complex / SNAP receptor activity / vesicle docking involved in exocytosis / apical dendrite ...Intra-Golgi traffic / protein-cysteine S-palmitoyltransferase activity / COPI-mediated anterograde transport / vesicle targeting / basal dendrite / COPII-mediated vesicle transport / SNARE complex / SNAP receptor activity / vesicle docking involved in exocytosis / apical dendrite / retrograde transport, endosome to Golgi / plasma membrane => GO:0005886 / endoplasmic reticulum to Golgi vesicle-mediated transport / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasmic vesicle membrane / protein transport / endosome / Golgi membrane / neuronal cell body / Golgi apparatus / endoplasmic reticulum / mitochondrion / membrane / cytosol / cytoplasm
Similarity search - Function
Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. ...Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Longin-like domain superfamily / Beta-Lactamase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
dodecyl 2-(trimethylammonio)ethyl phosphate / Synaptobrevin homolog YKT6
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.443 Å
AuthorsYu, J. / Wen, W.Y. / Zhang, M.J.
CitationJournal: Mol.Cell / Year: 2010
Title: Lipid-Induced Conformational Switch Controls Fusion Activity of Longin Domain SNARE Ykt6
Authors: Wen, W.Y. / Yu, J. / Pan, L.F. / Wei, Z.Y. / Weng, J.W. / Wang, W.N. / Ong, Y.S. / Tran, T.H.T. / Hong, W.J. / Zhang, M.J.
History
DepositionDec 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptobrevin homolog YKT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0554
Polymers22,5121
Non-polymers5443
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.810, 59.710, 108.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

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Components

#1: Protein Synaptobrevin homolog YKT6 / YKT6


Mass: 22511.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ykt6 / Plasmid: modified pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q5EGY4, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DPV / dodecyl 2-(trimethylammonio)ethyl phosphate / dodecylphosphocholine


Mass: 351.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H38NO4P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND DPV (DODECYLPHOSPHOCHOLINE) IS DESCRIBED AS DPC IN THE ARTICLE.

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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: 1.97 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2M (NH4)2SO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.443→30 Å / Num. all: 6900 / Num. obs: 6788 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 10
Reflection shellResolution: 2.443→2.506 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BW6

3bw6


Resolution: 2.443→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.885 / SU B: 18.161 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26137 683 9.9 %RANDOM
Rwork0.1994 ---
obs0.20516 6195 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.673 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--1.11 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.443→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 0 33 86 1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221599
X-RAY DIFFRACTIONr_angle_refined_deg1.061.9872155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3695192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73123.94471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48615289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7321510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021163
X-RAY DIFFRACTIONr_nbd_refined0.1870.2658
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21078
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.213
X-RAY DIFFRACTIONr_mcbond_it0.6051.5990
X-RAY DIFFRACTIONr_mcangle_it0.93621557
X-RAY DIFFRACTIONr_scbond_it0.983675
X-RAY DIFFRACTIONr_scangle_it1.5814.5598
LS refinement shellResolution: 2.443→2.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 57 -
Rwork0.229 451 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: -9.4557 Å / Origin y: 6.7386 Å / Origin z: 14.9936 Å
111213212223313233
T-0.0476 Å2-0.0125 Å2-0.0019 Å2--0.0265 Å2-0.0014 Å2---0.0147 Å2
L0.6711 °20.3304 °20.0767 °2-0.7845 °20.0328 °2--0.8022 °2
S-0.0237 Å °0.0645 Å °-0.0253 Å °-0.0423 Å °0.0234 Å °-0.0074 Å °-0.0352 Å °0.0036 Å °0.0003 Å °

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