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- PDB-5fjx: Yeast delta-COP-I mu-homology domain complexed with Gcs1 WxxF peptide -

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Basic information

Entry
Database: PDB / ID: 5fjx
TitleYeast delta-COP-I mu-homology domain complexed with Gcs1 WxxF peptide
Components
  • ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN GCS1
  • COATOMER SUBUNIT DELTA
KeywordsPROTEIN TRANSPORT / COP-I / VESICLE COAT PROTEIN
Function / homology
Function and homology information


: / Golgi localization / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / Golgi to plasma membrane protein transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / GTPase activator activity / trans-Golgi network ...: / Golgi localization / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / Golgi to plasma membrane protein transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / GTPase activator activity / trans-Golgi network / protein transport / actin binding / cytoskeleton / endosome / Golgi membrane / perinuclear region of cytoplasm / mitochondrion / metal ion binding / cytosol
Similarity search - Function
Coatomer delta subunit / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain ...Coatomer delta subunit / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / 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
ADP-ribosylation factor GTPase-activating protein GCS1 / Coatomer subunit delta
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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: ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN GCS1
E: ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN GCS1


Theoretical massNumber of molelcules
Total (without water)92,1935
Polymers92,1935
Non-polymers00
Water4,648258
1
A: COATOMER SUBUNIT DELTA
E: ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN GCS1


Theoretical massNumber of molelcules
Total (without water)31,0882
Polymers31,0882
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-4.3 kcal/mol
Surface area13660 Å2
MethodPISA
2
B: COATOMER SUBUNIT DELTA
D: ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN GCS1


Theoretical massNumber of molelcules
Total (without water)31,0882
Polymers31,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-3.6 kcal/mol
Surface area13570 Å2
MethodPISA
3
C: COATOMER SUBUNIT DELTA


Theoretical massNumber of molelcules
Total (without water)30,0181
Polymers30,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.765, 84.855, 148.640
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 COATOMER SUBUNIT DELTA / DELTA-COAT PROTEIN / DELTA-COP


Mass: 30017.650 Da / Num. of mol.: 3 / Fragment: MU-HOMOLOGY DOMAIN, RESIDUES 3282-546 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P43621
#2: Protein/peptide ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN GCS1 / ARF GAP GCS1


Mass: 1070.043 Da / Num. of mol.: 2 / Fragment: RESIDUES 345-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P35197
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.57 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1M TRIS-HCL PH8.5, 0.2M MGCL2, 30% PEG-4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.45→56 Å / Num. obs: 33682 / % possible obs: 99.9 % / Observed criterion σ(I): 99 / Redundancy: 6.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FJW

5fjw


Resolution: 2.45→74.32 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.877 / SU B: 11.984 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R: 0.52 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28742 1745 5.2 %RANDOM
Rwork0.1971 ---
obs0.20156 31880 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.115 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2---0.12 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.45→74.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 0 0 258 6479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196371
X-RAY DIFFRACTIONr_bond_other_d0.0020.026026
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9778656
X-RAY DIFFRACTIONr_angle_other_deg0.967313978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4735806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23626.109293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.247151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0211522
X-RAY DIFFRACTIONr_chiral_restr0.090.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217188
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021308
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_it3.9895.8053197
X-RAY DIFFRACTIONr_mcbond_other3.9835.8043196
X-RAY DIFFRACTIONr_mcangle_it6.2438.6953991
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0326.1753174
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: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 154 -
Rwork0.304 2297 -
obs--99.72 %

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