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- PDB-8ftu: Crystal structure of the SNARE Use1 bound to Dsl1 complex subunit... -

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Basic information

Entry
Database: PDB / ID: 8ftu
TitleCrystal structure of the SNARE Use1 bound to Dsl1 complex subunits Sec39 and Dsl1, Revised Use1 structure
Components
  • Protein transport protein DSL1
  • Protein transport protein SEC39
  • Vesicle transport protein USE1
KeywordsTRANSPORT PROTEIN / membrane trafficking / SNARE protein / COPI / vesicle / multisubunit tethering complex / Dsl1 complex / CATCHR complex
Function / homology
Function and homology information


retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein transport / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Vesicle transport protein, Use1 / Membrane fusion protein Use1 / Sec39 domain / Secretory pathway protein Sec39 / Retrograde transport protein Dsl1 N-terminal domain / Retrograde transport protein Dsl1, C-terminal domain / Dsl1, N-terminal domain superfamily / Zw10/DSL1, C-terminal / Retrograde transport protein Dsl1 N terminal / Retrograde transport protein Dsl1 C terminal
Similarity search - Domain/homology
KLLA0F06644p / KLLA0C02695p / KLLA0B05115p
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.73 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
Citation
Journal: Nat Struct Mol Biol / Year: 2024
Title: Structure of a membrane tethering complex incorporating multiple SNAREs.
Authors: Kevin A DAmico / Abigail E Stanton / Jaden D Shirkey / Sophie M Travis / Philip D Jeffrey / Frederick M Hughson /
Abstract: Most membrane fusion reactions in eukaryotic cells are mediated by multisubunit tethering complexes (MTCs) and SNARE proteins. MTCs are much larger than SNAREs and are thought to mediate the initial ...Most membrane fusion reactions in eukaryotic cells are mediated by multisubunit tethering complexes (MTCs) and SNARE proteins. MTCs are much larger than SNAREs and are thought to mediate the initial attachment of two membranes. Complementary SNAREs then form membrane-bridging complexes whose assembly draws the membranes together for fusion. Here we present a cryo-electron microscopy structure of the simplest known MTC, the 255-kDa Dsl1 complex of Saccharomyces cerevisiae, bound to the two SNAREs that anchor it to the endoplasmic reticulum. N-terminal domains of the SNAREs form an integral part of the structure, stabilizing a Dsl1 complex configuration with unexpected similarities to the 850-kDa exocyst MTC. The structure of the SNARE-anchored Dsl1 complex and its comparison with exocyst reveal what are likely to be common principles underlying MTC function. Our structure also implies that tethers and SNAREs can work together as a single integrated machine.
#1: Journal: 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
DepositionJan 13, 2023Deposition site: RCSB / Processing site: RCSB
SupersessionMar 1, 2023ID: 6WC4
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein transport protein SEC39
B: Vesicle transport protein USE1
C: Protein transport protein DSL1


Theoretical massNumber of molelcules
Total (without water)129,1363
Polymers129,1363
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-27 kcal/mol
Surface area51750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.790, 87.846, 161.431
Angle α, β, γ (deg.)90.00, 107.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein transport protein SEC39


Mass: 79860.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_B05115g / Plasmid: pQLinkH / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6CWC7
#2: Protein Vesicle transport protein USE1


Mass: 13260.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_F06644g / Plasmid: pQLinkH / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6CL08
#3: Protein Protein transport protein DSL1


Mass: 36014.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_C02695g / Plasmid: pQLinkH / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6CUS2

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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: 6.88 Å3/Da / Density % sol: 80.48 % / Description: thin rectangular plates, 200 x 200 x 20 um
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris, pH 7.5, 0.1 M NaCl, 8% (w/v) PEG 3350, 10% (v/v) ethylene glycol, 1 mM dithiothreitol. Cryoprotected with 30% (v/v) ethylene glycol

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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: 0.97932 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 14, 2018
RadiationMonochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 5.726→29.601 Å / Num. obs: 7053 / % possible obs: 74.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 317.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.07 / Rrim(I) all: 0.135 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
5.726-6.6456.41.8141.110080.3191.1842.17129.8
12.006-29.6016.70.05226.410070.9970.0320.061100

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660-000refinement
XDSdata reduction
Aimless0.7.3data scaling
STARANISO2.0.8data scaling
PHASER2.8.3phasing
PDB_EXTRACT4data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 5.73→29.6 Å / SU ML: 1.06 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 40.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 703 9.99 %
Rwork0.2759 --
obs0.2782 7036 74.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.73→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8254 0 0 0 8254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148410
X-RAY DIFFRACTIONf_angle_d1.85611381
X-RAY DIFFRACTIONf_dihedral_angle_d26.1193152
X-RAY DIFFRACTIONf_chiral_restr0.0931318
X-RAY DIFFRACTIONf_plane_restr0.0121433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.73-6.160.3472200.4503187X-RAY DIFFRACTION11
6.16-6.780.42691160.39621033X-RAY DIFFRACTION61
6.78-7.740.38051860.34961679X-RAY DIFFRACTION100
7.74-9.70.29861900.26111699X-RAY DIFFRACTION100
9.7-29.60.25651910.24111735X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 9.1493 Å / Origin y: 40.5827 Å / Origin z: -30.9085 Å
111213212223313233
T1.5118 Å2-0.1687 Å20.4767 Å2-2.9094 Å2-0.0933 Å2--2.3294 Å2
L0.0895 °20.1443 °21.4967 °2--0.0833 °20.4588 °2--3.421 °2
S-0.5382 Å °0.0509 Å °-0.0973 Å °-0.6452 Å °-0.0569 Å °0.1933 Å °-1.4366 Å °0.1049 Å °-0.1822 Å °
Refinement TLS groupSelection details: all

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