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- PDB-4j86: Crystal structure of beta'-COP/yWbp1 complex -

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Basic information

Entry
Database: PDB / ID: 4j86
TitleCrystal structure of beta'-COP/yWbp1 complex
Components
  • Coatomer subunit beta'
  • Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1
KeywordsPROTEIN TRANSPORT / Beta propeller / dilysine motif / ER retrieval
Function / homology
Function and homology information


COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / oligosaccharyltransferase complex / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / protein N-linked glycosylation via asparagine / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein N-linked glycosylation ...COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / oligosaccharyltransferase complex / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / protein N-linked glycosylation via asparagine / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein N-linked glycosylation / glycosyltransferase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / Neutrophil degranulation / ubiquitin binding / intracellular protein transport / nuclear envelope / Golgi membrane / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum
Similarity search - Function
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit / Oligosaccharyltransferase 48 kDa subunit beta / 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. ...Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit / Oligosaccharyltransferase 48 kDa subunit beta / 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
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 / Coatomer subunit beta'
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsMa, W. / Goldberg, J.
CitationJournal: Embo J. / Year: 2013
Title: Rules for the recognition of dilysine retrieval motifs by coatomer.
Authors: Ma, W. / Goldberg, J.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coatomer subunit beta'
B: Coatomer subunit beta'
C: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1
D: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1


Theoretical massNumber of molelcules
Total (without water)70,0674
Polymers70,0674
Non-polymers00
Water12,701705
1
A: Coatomer subunit beta'
C: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1


Theoretical massNumber of molelcules
Total (without water)35,0342
Polymers35,0342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coatomer subunit beta'
D: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1


Theoretical massNumber of molelcules
Total (without water)35,0342
Polymers35,0342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.9760, 50.6480, 83.5760
Angle α, β, γ (deg.)90.0000, 99.4590, 90.0000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Coatomer subunit beta' / Beta'-coat protein / Beta'-COP


Mass: 34293.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41811
#2: Protein/peptide Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 / Oligosaccharyl transferase subunit WBP1 / Oligosaccharyl transferase subunit beta


Mass: 739.859 Da / Num. of mol.: 2 / Fragment: UNP residues 425-430 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33767
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.2 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.48→43.1 Å / Num. all: 102049 / Num. obs: 102029 / % possible obs: 99.4 % / Observed criterion σ(I): 2.6

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Processing

Software
NameVersionClassification
ADSCdata collection
PHENIX(phenix.refine: 1.8_1069)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→43.1 Å / σ(F): 2.6 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.188 4884 RANDOM
Rwork0.163 --
obs0.163 102029 -
all-102049 -
Refinement stepCycle: LAST / Resolution: 1.48→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4913 0 0 705 5618

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