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- PDB-4j8b: Crystal structure of alpha-COP/Emp47p complex -

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Basic information

Entry
Database: PDB / ID: 4j8b
TitleCrystal structure of alpha-COP/Emp47p complex
Components
  • Emp47p
  • coatomer alpha subunit
KeywordsPROTEIN TRANSPORT / beta propeller domain / Dilysine motif / ER retrieval
Function / homology
Function and homology information


COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity ...COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity / Golgi apparatus / cytoplasm
Similarity search - Function
Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / YVTN repeat-like/Quinoprotein amine dehydrogenase ...Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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
Putative coatomer subunit alpha
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.878 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

Downloads & links

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Assembly

Deposited unit
A: coatomer alpha subunit
B: Emp47p


Theoretical massNumber of molelcules
Total (without water)38,2432
Polymers38,2432
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint1 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.743, 81.958, 87.227
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 alpha subunit


Mass: 37525.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q96WV5
#2: Protein/peptide Emp47p


Mass: 716.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.32 Å3/Da / Density % sol: 47.09 %

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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: 1.878→77.105 Å / Num. all: 33643 / Num. obs: 29390 / % possible obs: 98.8 % / Observed criterion σ(I): 2.4

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Processing

Software
NameVersionClassification
ADSCdata collection
PHENIX(phenix.refine: 1.8_1069)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.878→59.729 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 1992 6.78 %
Rwork0.1762 --
obs0.1789 29390 98.5 %
all-33643 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.878→59.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 0 163 2620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082568
X-RAY DIFFRACTIONf_angle_d1.3563485
X-RAY DIFFRACTIONf_dihedral_angle_d14.159907
X-RAY DIFFRACTIONf_chiral_restr0.1376
X-RAY DIFFRACTIONf_plane_restr0.005439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.878-1.92460.24341360.22181913X-RAY DIFFRACTION98
1.9246-1.97670.2461370.2081915X-RAY DIFFRACTION98
1.9767-2.03480.23191450.19721896X-RAY DIFFRACTION97
2.0348-2.10050.24651430.18141952X-RAY DIFFRACTION100
2.1005-2.17560.24111410.18911966X-RAY DIFFRACTION100
2.1756-2.26270.21121500.17911933X-RAY DIFFRACTION99
2.2627-2.36570.23411320.17431955X-RAY DIFFRACTION98
2.3657-2.49040.24861540.19041901X-RAY DIFFRACTION97
2.4904-2.64640.24571360.18961965X-RAY DIFFRACTION100
2.6464-2.85080.24391410.18261956X-RAY DIFFRACTION99
2.8508-3.13760.20391460.16851965X-RAY DIFFRACTION98
3.1376-3.59160.20931370.15731991X-RAY DIFFRACTION99
3.5916-4.52480.18781460.15121989X-RAY DIFFRACTION98
4.5248-59.75920.21141480.19372101X-RAY DIFFRACTION98

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