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- PDB-3k8p: Structural basis for vesicle tethering by the Dsl1 complex -

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Basic information

Entry
Database: PDB / ID: 3k8p
TitleStructural basis for vesicle tethering by the Dsl1 complex
Components
  • Dsl1
  • Protein transport protein SEC39
KeywordsTRANSPORT PROTEIN/TRANSPORT PROTEIN / Intracellular trafficking / Dsl1 complex / multisubunit tethering complex / SNARE proteins / Endoplasmic reticulum / ER-Golgi transport / Membrane / Protein transport / Transport / TRANSPORT PROTEIN-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


ER-dependent peroxisome organization / Dsl1/NZR complex / RZZ complex / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / mitotic spindle assembly checkpoint signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / nuclear envelope / protein transport / endoplasmic reticulum membrane ...ER-dependent peroxisome organization / Dsl1/NZR complex / RZZ complex / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / mitotic spindle assembly checkpoint signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / nuclear envelope / protein transport / endoplasmic reticulum membrane / endoplasmic reticulum / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1440 / Tetracycline Repressor; domain 2 - #150 / 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 / Retrograde transport protein Dsl1 N terminal / Retrograde transport protein Dsl1 C terminal / Zw10/DSL1, C-terminal ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1440 / Tetracycline Repressor; domain 2 - #150 / 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 / Retrograde transport protein Dsl1 N terminal / Retrograde transport protein Dsl1 C terminal / Zw10/DSL1, C-terminal / Tetracycline Repressor; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein transport protein SEC39 / KLLA0C02695p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsRen, Y. / Jeffrey, P.D. / Hughson, F.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: A structure-based mechanism for vesicle capture by the multisubunit tethering complex Dsl1.
Authors: Ren, Y. / Yip, C.K. / Tripathi, A. / Huie, D. / Jeffrey, P.D. / Walz, T. / Hughson, F.M.
History
DepositionOct 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Dsl1
D: Protein transport protein SEC39


Theoretical massNumber of molelcules
Total (without water)125,6212
Polymers125,6212
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-14 kcal/mol
Surface area44350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.020, 90.820, 213.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dsl1 / KLLA0C02695p


Mass: 42387.000 Da / Num. of mol.: 1 / Fragment: UNP residues 332-686
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0C02695g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CUS2
#2: Protein Protein transport protein SEC39 / Dependent on SLY1-20 protein 3


Mass: 83234.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC39, DSL3, YLR440C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12745
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 10% PEG monomethyl ether 5000, 0.1 M MgCl2, 5% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793, 0.9795, 0.9641
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2008
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.96411
ReflectionResolution: 2.6→50 Å / Num. obs: 82563 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.06
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rsym value: 0.421 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→31.197 Å / SU ML: 0.37 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 3943 5.02 %RANDOM
Rwork0.2049 ---
obs0.2082 78583 94.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.898 Å2 / ksol: 0.326 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→31.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7373 0 0 3 7376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087521
X-RAY DIFFRACTIONf_angle_d1.14110160
X-RAY DIFFRACTIONf_dihedral_angle_d19.2352792
X-RAY DIFFRACTIONf_chiral_restr0.0791156
X-RAY DIFFRACTIONf_plane_restr0.0041272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63370.28831270.24082393X-RAY DIFFRACTION85
2.6337-2.66710.37151140.26172525X-RAY DIFFRACTION88
2.6671-2.70210.36391250.27322479X-RAY DIFFRACTION89
2.7021-2.73910.33841270.25232500X-RAY DIFFRACTION89
2.7391-2.77820.29851300.25442511X-RAY DIFFRACTION90
2.7782-2.81970.27641690.25152588X-RAY DIFFRACTION92
2.8197-2.86370.32561380.25482560X-RAY DIFFRACTION92
2.8637-2.91060.38361270.2612619X-RAY DIFFRACTION92
2.9106-2.96080.37671220.26022638X-RAY DIFFRACTION93
2.9608-3.01460.35181680.24832652X-RAY DIFFRACTION94
3.0146-3.07250.29041340.23212636X-RAY DIFFRACTION94
3.0725-3.13520.34181550.22482733X-RAY DIFFRACTION95
3.1352-3.20330.2751190.22442660X-RAY DIFFRACTION95
3.2033-3.27770.31511570.23042714X-RAY DIFFRACTION97
3.2777-3.35960.32291690.22042712X-RAY DIFFRACTION97
3.3596-3.45030.30471530.20852727X-RAY DIFFRACTION98
3.4503-3.55170.23161140.18542802X-RAY DIFFRACTION98
3.5517-3.66620.25661610.18852754X-RAY DIFFRACTION98
3.6662-3.7970.26311490.18422810X-RAY DIFFRACTION99
3.797-3.94870.23391430.18122772X-RAY DIFFRACTION98
3.9487-4.12810.22251430.17522795X-RAY DIFFRACTION99
4.1281-4.34520.23541310.15962782X-RAY DIFFRACTION98
4.3452-4.61660.22111490.1542769X-RAY DIFFRACTION99
4.6166-4.97170.20951330.1462800X-RAY DIFFRACTION99
4.9717-5.46960.21241440.16522766X-RAY DIFFRACTION98
5.4696-6.25560.27531480.1922679X-RAY DIFFRACTION96
6.2556-7.86040.2321400.19822661X-RAY DIFFRACTION94
7.8604-31.19880.21511540.19182603X-RAY DIFFRACTION93
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined1.29290.1467-0.60980.6986-0.04871.4345-0.11830.335-0.2964-0.482-0.2195-0.20430.70540.01560.25150.59630.01450.1540.1866-0.00050.301215.219621.8237116.974
21.5872-0.4432-0.22262.2935-1.19071.4992-0.03040.0861-0.00580.0656-0.07280.1066-0.03510.16160.07920.04910.01110.04930.15820.03160.119
31.341-0.5672-0.22421.2910.14781.1349-0.0842-0.5410.2990.09630.274-0.026-0.196-0.3727-0.13260.22710.17460.06890.5152-0.10610.4069
40.6013-0.00890.60450.39130.40235.18320.01450.1095-0.14320.04930.0821-0.0486-0.00620.1762-0.09920.0576-0.0157-0.00350.1541-0.04340.1758
51.0052-0.3272-0.1023-0.12180.27753.4707-0.103-0.10620.12860.0037-0.0047-0.1004-0.0406-0.06170.09190.4326-0.11560.05680.202-0.03620.2434
Refinement TLS groupSelection details: chain D and resid 512:684

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