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- PDB-5fjw: Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWx(MSE... -

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Basic information

Entry
Database: PDB / ID: 5fjw
TitleYeast delta-COP-I mu-homology domain complexed with Dsl1 WxWx(MSE) peptide
Components
  • COATOMER SUBUNIT DELTA
  • PROTEIN TRANSPORT PROTEIN DSL1
KeywordsPROTEIN TRANSPORT / COP-I / VESICLE COAT PROTEIN
Function / homology
Function and homology information


Golgi distribution to daughter cells / ER-dependent peroxisome organization / Dsl1/NZR complex / RZZ complex / Golgi localization / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / Golgi inheritance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...Golgi distribution to daughter cells / ER-dependent peroxisome organization / Dsl1/NZR complex / RZZ complex / Golgi localization / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / Golgi inheritance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / mitotic spindle assembly checkpoint signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / nucleus / cytosol
Similarity search - Function
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 / Coatomer delta subunit / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain ...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 / Coatomer delta subunit / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily
Similarity search - Domain/homology
Coatomer subunit delta / Protein transport protein DSL1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSuckling, R.J. / Evans, P.R. / Owen, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural Basis for the Binding of Tryptophan-Based Motifs by Delta-Cop.
Authors: Suckling, R.J. / Poon, P.P. / Travis, S.M. / Majoul, I.V. / Hughson, F.M. / Evans, P.R. / Duden, R. / Owen, D.J.
History
DepositionOct 13, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Mar 2, 2016Group: Data collection / Refinement description
Revision 1.3Apr 6, 2016Group: Data collection
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COATOMER SUBUNIT DELTA
B: COATOMER SUBUNIT DELTA
C: COATOMER SUBUNIT DELTA
D: COATOMER SUBUNIT DELTA
E: COATOMER SUBUNIT DELTA
F: COATOMER SUBUNIT DELTA
G: COATOMER SUBUNIT DELTA
H: COATOMER SUBUNIT DELTA
L: PROTEIN TRANSPORT PROTEIN DSL1
M: PROTEIN TRANSPORT PROTEIN DSL1
N: PROTEIN TRANSPORT PROTEIN DSL1
O: PROTEIN TRANSPORT PROTEIN DSL1
P: PROTEIN TRANSPORT PROTEIN DSL1
Q: PROTEIN TRANSPORT PROTEIN DSL1
R: PROTEIN TRANSPORT PROTEIN DSL1
S: PROTEIN TRANSPORT PROTEIN DSL1


Theoretical massNumber of molelcules
Total (without water)250,43016
Polymers250,43016
Non-polymers00
Water9,980554
1
A: COATOMER SUBUNIT DELTA
L: PROTEIN TRANSPORT PROTEIN DSL1


Theoretical massNumber of molelcules
Total (without water)31,3042
Polymers31,3042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-7.2 kcal/mol
Surface area13540 Å2
MethodPISA
2
F: COATOMER SUBUNIT DELTA
Q: PROTEIN TRANSPORT PROTEIN DSL1


Theoretical massNumber of molelcules
Total (without water)31,3042
Polymers31,3042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7.3 kcal/mol
Surface area13470 Å2
MethodPISA
3
H: COATOMER SUBUNIT DELTA
S: PROTEIN TRANSPORT PROTEIN DSL1


Theoretical massNumber of molelcules
Total (without water)31,3042
Polymers31,3042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7.6 kcal/mol
Surface area13590 Å2
MethodPISA
4
E: COATOMER SUBUNIT DELTA
P: PROTEIN TRANSPORT PROTEIN DSL1


Theoretical massNumber of molelcules
Total (without water)31,3042
Polymers31,3042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-6 kcal/mol
Surface area13480 Å2
MethodPISA
5
D: COATOMER SUBUNIT DELTA
O: PROTEIN TRANSPORT PROTEIN DSL1


Theoretical massNumber of molelcules
Total (without water)31,3042
Polymers31,3042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-5.6 kcal/mol
Surface area13660 Å2
MethodPISA
6
G: COATOMER SUBUNIT DELTA
R: PROTEIN TRANSPORT PROTEIN DSL1


Theoretical massNumber of molelcules
Total (without water)31,3042
Polymers31,3042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-6.6 kcal/mol
Surface area13720 Å2
MethodPISA
7
B: COATOMER SUBUNIT DELTA
M: PROTEIN TRANSPORT PROTEIN DSL1


Theoretical massNumber of molelcules
Total (without water)31,3042
Polymers31,3042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-6.3 kcal/mol
Surface area13550 Å2
MethodPISA
8
C: COATOMER SUBUNIT DELTA
N: PROTEIN TRANSPORT PROTEIN DSL1


Theoretical massNumber of molelcules
Total (without water)31,3042
Polymers31,3042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-5.7 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.406, 79.298, 163.346
Angle α, β, γ (deg.)79.71, 87.50, 83.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
COATOMER SUBUNIT DELTA / DELTA-COAT PROTEIN / DELTA-COP


Mass: 30017.650 Da / Num. of mol.: 8 / Fragment: MU-HOMOLOGY DOMAIN, RESIDUES 288-516 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Gene: RET2, YFR051C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P43621
#2: Protein/peptide
PROTEIN TRANSPORT PROTEIN DSL1 / DEPENDENT ON SLY1-20 PROTEIN 1


Mass: 1286.120 Da / Num. of mol.: 8 / Fragment: WXW MOTIF, RESIDUES 411-419 / Source method: obtained synthetically / Details: MSE IN PLACE OF MET / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P53847
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsW404 MUTANT SEMET IN PLACE OF MET

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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: 3.46 Å3/Da / Density % sol: 64.44 % / Description: NONE
Crystal growpH: 7
Details: 0.1MHEPES-NA PH 7.0, 0.15M(NH4)2SO4, 21%W/V PEG2250

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631, 0.97949, 0.97961
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976311
20.979491
30.979611
ReflectionResolution: 2.8→77.6 Å / Num. obs: 80910 / % possible obs: 97.8 % / Observed criterion σ(I): 99 / Redundancy: 7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.1 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.8→160.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.889 / SU B: 17.512 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 0.839 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23949 4059 5 %RANDOM
Rwork0.17037 ---
obs0.17385 76851 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.088 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å2-2.1 Å2-1.66 Å2
2--3.17 Å25.34 Å2
3----3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.8→160.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17032 0 0 554 17586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01917480
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216383
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.97223772
X-RAY DIFFRACTIONr_angle_other_deg0.993338002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.93652204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12926.244828
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.689152917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.141557
X-RAY DIFFRACTIONr_chiral_restr0.0970.22767
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119803
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023612
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.2378.5598732
X-RAY DIFFRACTIONr_mcbond_other6.2358.5598731
X-RAY DIFFRACTIONr_mcangle_it9.86112.81610898
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.7419.1198748
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 279 -
Rwork0.37 5706 -
obs--97.46 %

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