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- PDB-4j84: Crystal structure of beta'-COP/Scyl1 complex -

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Basic information

Entry
Database: PDB / ID: 4j84
TitleCrystal structure of beta'-COP/Scyl1 complex
Components
  • Coatomer subunit beta'
  • SCYL1
KeywordsPROTEIN TRANSPORT / Beta propeller domain / RK motif / Vesicle trafficking / Golgi retention
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 / : / : / 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 ...Coatomer beta' subunit (COPB2) / 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 / 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
Coatomer subunit beta'
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.473 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: SCYL1
D: SCYL1


Theoretical massNumber of molelcules
Total (without water)69,7954
Polymers69,7954
Non-polymers00
Water14,160786
1
A: Coatomer subunit beta'
C: SCYL1


Theoretical massNumber of molelcules
Total (without water)34,8972
Polymers34,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coatomer subunit beta'
D: SCYL1


Theoretical massNumber of molelcules
Total (without water)34,8972
Polymers34,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.554, 46.155, 84.300
Angle α, β, γ (deg.)81.46, 81.96, 69.47
Int Tables number1
Space group name H-MP1

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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 SCYL1


Mass: 603.712 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 786 / 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: 2.19 Å3/Da / Density % sol: 43.76 %

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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: 1.47→50 Å / Num. all: 93131 / Num. obs: 93130 / % possible obs: 93.5 % / Observed criterion σ(I): 2.5

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Processing

Software
NameVersionClassification
ADSCdata collection
PHENIX(phenix.refine: 1.7.3_928)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.473→39.952 Å / SU ML: 0.18 / σ(F): 1.97 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1990 2.14 %RANDOM
Rwork0.188 ---
obs0.1884 93112 93.1 %-
all-93131 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.609 Å2 / ksol: 0.408 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8693 Å2-1.5973 Å20.1095 Å2
2---1.9487 Å22.1658 Å2
3----1.9207 Å2
Refinement stepCycle: LAST / Resolution: 1.473→39.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4843 0 0 786 5629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064960
X-RAY DIFFRACTIONf_angle_d1.1716757
X-RAY DIFFRACTIONf_dihedral_angle_d12.0451759
X-RAY DIFFRACTIONf_chiral_restr0.082750
X-RAY DIFFRACTIONf_plane_restr0.006850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.473-1.50990.30551390.26896092X-RAY DIFFRACTION88
1.5099-1.55070.27621400.23286590X-RAY DIFFRACTION94
1.5507-1.59630.2351420.21566636X-RAY DIFFRACTION95
1.5963-1.64780.26611440.19696653X-RAY DIFFRACTION95
1.6478-1.70670.20161420.18766660X-RAY DIFFRACTION95
1.7067-1.77510.21520.18076696X-RAY DIFFRACTION95
1.7751-1.85590.18161350.17486670X-RAY DIFFRACTION96
1.8559-1.95370.22251470.17346698X-RAY DIFFRACTION96
1.9537-2.07610.19811500.17926674X-RAY DIFFRACTION96
2.0761-2.23640.20261410.18056700X-RAY DIFFRACTION96
2.2364-2.46140.21321430.18136735X-RAY DIFFRACTION96
2.4614-2.81750.22311610.19216705X-RAY DIFFRACTION95
2.8175-3.54940.16061370.18246291X-RAY DIFFRACTION90
3.5494-39.96670.2011170.1855322X-RAY DIFFRACTION76

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