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- PDB-8d30: Crystal structure of the human COPB2 WD-domains -

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Basic information

Entry
Database: PDB / ID: 8d30
TitleCrystal structure of the human COPB2 WD-domains
ComponentsCoatomer subunit beta'
KeywordsTRANSPORT PROTEIN / WD-repeat / WDR / COPB2 / coatomer subunit beta / SGC / Structural Genomics / Structural Genomics Consortium / ER-Golgi transport
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 / endoplasmic reticulum 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 / : / COPA/B second beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. ...Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / : / COPA/B second beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD domain, G-beta repeat / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Crystal structure of the human COPB2 WD-domains
Authors: Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionMay 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,0683
Polymers140,0062
Non-polymers621
Water1,44180
1
A: Coatomer subunit beta'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0652
Polymers70,0031
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)70,0031
Polymers70,0031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.074, 134.062, 144.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 70003.141 Da / Num. of mol.: 2 / Fragment: COPB2 WD-domains
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 46.9 % / Mosaicity: 0.407 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20%(w/v) PEG 3350, 0.05M Magnesium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 51291 / % possible obs: 99 % / Redundancy: 5.6 % / Biso Wilson estimate: 62.71 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.037 / Rrim(I) all: 0.089 / Χ2: 1.173 / Net I/σ(I): 8.9 / Num. measured all: 288205
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.444.81.00524390.4960.4861.1230.92897.1
2.44-2.495.60.92225820.6040.4221.0170.94199.6
2.49-2.535.90.8425390.6950.3750.9220.937100
2.53-2.595.90.72425660.7630.3240.7950.963100
2.59-2.645.90.6125180.8290.2720.6690.989100
2.64-2.75.90.47625900.8820.2130.5231.00799.9
2.7-2.775.80.37925390.9180.1710.4171.0299.9
2.77-2.855.80.32625590.9380.1470.3591.05499.8
2.85-2.935.80.25425530.9640.1150.2791.05699.6
2.93-3.025.70.20425660.9750.0930.2251.09899.9
3.02-3.135.60.15525730.9840.0710.1711.12899.8
3.13-3.265.50.11625710.9890.0530.1281.17799.8
3.26-3.415.30.09325530.9910.0440.1041.3199.1
3.41-3.584.90.07524800.9940.0370.0851.39195.9
3.58-3.815.60.06825420.9950.0310.0751.35698
3.81-4.160.05825820.9960.0260.0641.46699.2
4.1-4.525.90.04925950.9970.0220.0541.47799
4.52-5.175.80.04426190.9970.020.0491.39399
5.17-6.515.40.04526180.9980.0210.051.38998.4
6.51-505.40.03927070.9970.0180.0431.38996.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NZR

5nzr


Resolution: 2.4→49.12 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.365 / SU Rfree Blow DPI: 0.238 / SU Rfree Cruickshank DPI: 0.243
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2516 4.91 %RANDOM
Rwork0.219 ---
obs0.221 51241 98.7 %-
Displacement parametersBiso max: 179.31 Å2 / Biso mean: 61.26 Å2 / Biso min: 22.38 Å2
Baniso -1Baniso -2Baniso -3
1-4.0258 Å20 Å20 Å2
2--1.002 Å20 Å2
3----5.0278 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.4→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8454 0 4 80 8538
Biso mean--56.74 50.44 -
Num. residues----1136
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2735SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1479HARMONIC5
X-RAY DIFFRACTIONt_it8689HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1181SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9210SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8689HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11855HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion18.35
LS refinement shellResolution: 2.4→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.4594 51 4.98 %
Rwork0.2627 974 -
all0.2714 1025 -
obs--83.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.78390.8993-0.29391.086-0.08140.34170.1406-0.3039-0.10740.0719-0.1693-0.0390.05230.07570.0287-0.0693-0.0092-0.0441-0.01620.0268-0.1862-31.7612-27.313825.9353
24.40573.0718-2.7212.4855-1.82762.12320.05160.32580.6175-0.11270.21370.3516-0.0426-0.0701-0.2653-0.31390.0206-0.0523-0.27880.0848-0.1206-17.34798.9479-0.3919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 588
2X-RAY DIFFRACTION2{ B|* }B2 - 588

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