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- PDB-6wc3: Crystal structure of the SNARE Sec20 bound to Dsl1 complex subuni... -

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Basic information

Entry
Database: PDB / ID: 6wc3
TitleCrystal structure of the SNARE Sec20 bound to Dsl1 complex subunit Tip20
Components
  • Protein transport protein SEC20
  • Protein transport protein TIP20
KeywordsTRANSPORT PROTEIN / membrane trafficking / SNARE protein / COPI / vesicle / multisubunit tethering complex / Dsl1 complex / CATCHR complex
Function / homology
Function and homology information


Dsl1/NZR complex / regulation of ER to Golgi vesicle-mediated transport / SNARE complex / SNAP receptor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagy / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Sec20 / Sec20 / RINT-1/Tip20 / Protein transport protein Tip20, domain E / Protein transport protein Tip20, domain A / Protein transport protein Tip20, domain B / Protein transport protein Tip20, domain C / RINT-1/TIP-1 family / RINT1/TIP20 domain profile. / EXOC6/PINT-1/Sec15/Tip20, C-terminal, domain 2
Similarity search - Domain/homology
Biological speciesAshbya gossypii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.203 Å
AuthorsTravis, S.M. / Jeffrey, P.D. / Hughson, F.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM12676 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007388 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis for the binding of SNAREs to the multisubunit tethering complex Dsl1.
Authors: Travis, S.M. / DAmico, K. / Yu, I.M. / McMahon, C. / Hamid, S. / Ramirez-Arellano, G. / Jeffrey, P.D. / Hughson, F.M.
History
DepositionMar 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein transport protein TIP20
B: Protein transport protein SEC20


Theoretical massNumber of molelcules
Total (without water)84,1802
Polymers84,1802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-10 kcal/mol
Surface area34500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.275, 133.275, 288.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Protein transport protein TIP20 / ADL286Wp


Mass: 68547.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus)
Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: AGOS_ADL286W / Plasmid: pQLinkH / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q75B58
#2: Protein Protein transport protein SEC20 / AFR344Cp


Mass: 15632.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus)
Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: AGOS_AFR344C / Plasmid: pQLinkN / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q753G8

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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: 4.39 Å3/Da / Density % sol: 72 % / Description: rounded hexagonal, 100 x 100 x 100 um
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium citrate, pH 6.0, 0.725 M ammonium sulfate, 1 mM dithiothreitol, cryoprotected with 30% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 20, 2017
RadiationMonochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→29.26 Å / Num. obs: 25597 / % possible obs: 99 % / Redundancy: 26 % / Biso Wilson estimate: 85.28 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.026 / Rrim(I) all: 0.135 / Net I/σ(I): 27.6 / Num. measured all: 666066
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.2-3.2821.91.1743591916380.8780.2441.23.288.4
14.32-29.26200.032656732810.0070.0339088.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å28.29 Å
Translation3.2 Å28.29 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
PHASER2.5.5phasing
PHENIX1.13.2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FHN

3fhn


Resolution: 3.203→28.294 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 2000 7.84 %
Rwork0.2103 23525 -
obs0.2132 25525 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.6 Å2 / Biso mean: 79.4855 Å2 / Biso min: 33.91 Å2
Refinement stepCycle: final / Resolution: 3.203→28.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5482 0 0 0 5482
Num. residues----671
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.203-3.28280.37981250.3155147690
3.2828-3.37140.27721400.28721647100
3.3714-3.47040.31411410.26631656100
3.4704-3.58220.25851410.25171655100
3.5822-3.710.24441420.23711673100
3.71-3.85820.26681400.21981655100
3.8582-4.03330.24831440.22271684100
4.0333-4.24530.26161410.20081663100
4.2453-4.51030.24171430.19231683100
4.5103-4.85690.23451430.18931688100
4.8569-5.34270.26491460.20271709100
5.3427-6.1090.2671450.23651717100
6.109-7.67120.25041500.2241751100
7.6712-28.2940.19611590.16011868100

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