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- PDB-8d41: Crystal structure of the human COPB2 WD-domain in complex with OI... -

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Basic information

Entry
Database: PDB / ID: 8d41
TitleCrystal structure of the human COPB2 WD-domain in complex with OICR-6254
ComponentsCoatomer subunit beta'
KeywordsPROTEIN TRANSPORT / WD-repeat / WDR / COPB2 / Coatomer subunit beta / SGC / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


: / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / transport vesicle / intracellular protein transport / Golgi membrane ...: / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / transport vesicle / intracellular protein transport / Golgi membrane / endoplasmic reticulum membrane / structural molecule activity / cytosol
Similarity search - Function
Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / Coatomer WD associated region / G-protein beta WD-40 repeat / 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
Similarity search - Domain/homology
Chem-Q93 / Coatomer subunit beta'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZeng, H. / Saraon, P. / Dong, A. / Hutchinson, A. / Seitova, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the human COPB2 WD-domain in complex with OICR-6254
Authors: Zeng, H. / Saraon, P. / Dong, A. / Hutchinson, A. / Seitova, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
History
DepositionJun 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coatomer subunit beta'
B: Coatomer subunit beta'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7026
Polymers72,8422
Non-polymers8604
Water6,305350
1
A: Coatomer subunit beta'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9354
Polymers36,4211
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coatomer subunit beta'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7682
Polymers36,4211
Non-polymers3461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.015, 91.149, 58.716
Angle α, β, γ (deg.)90.000, 99.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Coatomer subunit beta' / Beta'-coat protein / Beta'-COP / p102


Mass: 36421.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPB2 / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35606
#2: Chemical ChemComp-Q93 / (1R,2R,3S,4S)-3-[4-(4-fluorophenyl)piperazine-1-carbonyl]bicyclo[2.2.1]heptane-2-carboxylic acid


Mass: 346.396 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23FN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.44 % / Mosaicity: 0.27 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% w/v PEG3350,0.1 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→48.92 Å / Num. obs: 38534 / % possible obs: 96.1 % / Redundancy: 4.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.062 / Rrim(I) all: 0.128 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.053.90.5341048126560.7790.3050.617390.1
8.93-48.873.80.04218194740.9870.0250.04929.798.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8D30

8d30


Resolution: 2→48.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.45 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1919 5 %RANDOM
Rwork0.1705 ---
obs0.173 36560 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.64 Å2 / Biso mean: 18.801 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20.15 Å2
2--0.54 Å2-0 Å2
3---1.1 Å2
Refinement stepCycle: final / Resolution: 2→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4824 0 31 351 5206
Biso mean--32.18 25.04 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135014
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174473
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.6336829
X-RAY DIFFRACTIONr_angle_other_deg1.2191.5810383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0455612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21122.627255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9715813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2041527
X-RAY DIFFRACTIONr_chiral_restr0.0610.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025619
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021075
LS refinement shellResolution: 2→2.049 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.227 158 -
Rwork0.241 2487 -
obs--89.57 %

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