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- PDB-2ynp: yeast betaprime COP 1-604 with KTKTN motif -

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Basic information

Entry
Database: PDB / ID: 2ynp
Titleyeast betaprime COP 1-604 with KTKTN motif
Components
  • COATOMER SUBUNIT BETA'
  • KTKTN MOTIF
KeywordsPROTEIN TRANSPORT / MEMBRANE TRAFFICKING / COPI-MEDIATED TRAFFICKING / DILYSINE MOTIFS
Function / homology
Function and homology information


COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding / intracellular protein transport ...COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding / intracellular protein transport / Golgi membrane / structural molecule activity
Similarity search - Function
Coatomer beta' subunit (COPB2) / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat ...Coatomer beta' subunit (COPB2) / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Coatomer subunit beta'
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.962 Å
AuthorsJackson, L.P. / Lewis, M. / Kent, H.M. / Edeling, M.A. / Evans, P.R. / Duden, R. / Owen, D.J.
CitationJournal: Dev.Cell / Year: 2012
Title: Molecular Basis for Recognition of Dilysine Trafficking Motifs by Copi.
Authors: Jackson, L.P. / Lewis, M. / Kent, H.M. / Edeling, M.A. / Evans, P.R. / Duden, R. / Owen, D.J.
History
DepositionOct 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COATOMER SUBUNIT BETA'
P: KTKTN MOTIF


Theoretical massNumber of molelcules
Total (without water)69,0112
Polymers69,0112
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint2.7 kcal/mol
Surface area32240 Å2
MethodPQS
Unit cell
Length a, b, c (Å)127.250, 127.250, 59.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein COATOMER SUBUNIT BETA' / BETA'-COAT PROTEIN / BETA'-COP


Mass: 68066.906 Da / Num. of mol.: 1 / Fragment: WD40-REPEAT DOMAIN, RESIDUES 1-604
Source method: isolated from a genetically manipulated source
Details: IN COMPLEX WITH KXKXX MOTIF
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PMWGST / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P41811
#2: Protein/peptide KTKTN MOTIF


Mass: 944.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 0.1M BICINE PH 9.0, 10% MPD

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 2, 2011
RadiationMonochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
Reflection twinOperator: -K,-H,L / Fraction: 0.4
ReflectionResolution: 2.96→63.6 Å / Num. obs: 22113 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 73.06 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8
Reflection shellResolution: 2.96→3.04 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2YNO, 3MKQ

2yno

3mkq


Resolution: 2.962→63.625 Å / SU ML: 0.55 / σ(F): 1.98 / Phase error: 32.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2943 1133 5.1 %
Rwork0.2396 --
obs0.2425 22113 99.34 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.987 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso mean: 73.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.712 Å20 Å20 Å2
2---5.712 Å20 Å2
3---11.4241 Å2
Refinement stepCycle: LAST / Resolution: 2.962→63.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4851 0 0 2 4853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094978
X-RAY DIFFRACTIONf_angle_d1.3816776
X-RAY DIFFRACTIONf_dihedral_angle_d16.1411758
X-RAY DIFFRACTIONf_chiral_restr0.094742
X-RAY DIFFRACTIONf_plane_restr0.005868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9617-3.09650.39361440.30332649X-RAY DIFFRACTION100
3.0965-3.25980.36151290.27152674X-RAY DIFFRACTION100
3.2598-3.4640.32051440.25152612X-RAY DIFFRACTION100
3.464-3.73140.32991270.23942638X-RAY DIFFRACTION99
3.7314-4.10690.30991500.23842600X-RAY DIFFRACTION99
4.1069-4.7010.25841430.21972588X-RAY DIFFRACTION98
4.701-5.92210.26021380.22142631X-RAY DIFFRACTION100
5.9221-63.63970.28291580.24612588X-RAY DIFFRACTION99

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