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- PDB-2ynn: yeast betaprime COP 1-304 with KTKTN motif -

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Basic information

Entry
Database: PDB / ID: 2ynn
Titleyeast betaprime COP 1-304 with KTKTN motif
Components
  • COATOMER SUBUNIT BETA'
  • KTKTN MOTIF
KeywordsPROTEIN TRANSPORT / PEPTIDE BINDING PROTEIN / MEMBRANE TRAFFICKING / COPI-MEDIATED TRAFFICKING / DILYSINE MOTIFS
Function / homology
Function and homology information


COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / 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 vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / 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) / Coatomer, WD associated region / : / Coatomer WD associated region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. ...Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / : / Coatomer WD associated region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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: 1.782 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 / 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,8845
Polymers35,5962
Non-polymers2883
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint1.5 kcal/mol
Surface area14750 Å2
MethodPISA
2
A: COATOMER SUBUNIT BETA'
hetero molecules

P: KTKTN MOTIF


Theoretical massNumber of molelcules
Total (without water)35,8845
Polymers35,5962
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x+y-1,-x,z-1/31
Buried area1300 Å2
ΔGint-46.6 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.160, 129.160, 60.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 34651.953 Da / Num. of mol.: 1 / Fragment: WD40-REPEAT DOMAIN, RESIDUES 1-304
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growDetails: 0.1M HEPES PH 7.5, 0.5M AMMONIUM SULFATE, 30% V/V 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
ReflectionResolution: 1.73→56 Å / Num. obs: 54637 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 14.12 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.7
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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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 ENTRY 2YNO

2yno


Resolution: 1.782→55.928 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 16.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1799 2774 5.1 %
Rwork0.1621 --
obs0.163 54637 99.96 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.27 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.4738 Å20 Å20 Å2
2--0.4738 Å20 Å2
3----0.9476 Å2
Refinement stepCycle: LAST / Resolution: 1.782→55.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 15 231 2724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072623
X-RAY DIFFRACTIONf_angle_d1.2063590
X-RAY DIFFRACTIONf_dihedral_angle_d12.817952
X-RAY DIFFRACTIONf_chiral_restr0.09398
X-RAY DIFFRACTIONf_plane_restr0.006452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7824-1.81310.22891540.2122567X-RAY DIFFRACTION100
1.8131-1.84610.24511490.20372556X-RAY DIFFRACTION100
1.8461-1.88160.22431360.19372579X-RAY DIFFRACTION100
1.8816-1.920.20091350.17882593X-RAY DIFFRACTION100
1.92-1.96180.1951400.16842581X-RAY DIFFRACTION100
1.9618-2.00740.17661340.16262575X-RAY DIFFRACTION100
2.0074-2.05760.18571500.15972563X-RAY DIFFRACTION100
2.0576-2.11330.19661380.16132575X-RAY DIFFRACTION100
2.1133-2.17540.19751220.16212600X-RAY DIFFRACTION100
2.1754-2.24570.18411410.15952558X-RAY DIFFRACTION100
2.2457-2.32590.19621330.1642618X-RAY DIFFRACTION100
2.3259-2.41910.20251330.15822598X-RAY DIFFRACTION100
2.4191-2.52920.17991430.16872575X-RAY DIFFRACTION100
2.5292-2.66250.19981290.1732586X-RAY DIFFRACTION100
2.6625-2.82930.1711340.16812604X-RAY DIFFRACTION100
2.8293-3.04770.18971430.16622606X-RAY DIFFRACTION100
3.0477-3.35440.19121410.1632610X-RAY DIFFRACTION100
3.3544-3.83970.1651310.14312616X-RAY DIFFRACTION100
3.8397-4.83720.11641470.12842616X-RAY DIFFRACTION100
4.8372-55.95540.17561410.17462687X-RAY DIFFRACTION100

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