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- PDB-6pbg: Crystal structure of WD-repeat domain of human coatomer subunit A... -

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Basic information

Entry
Database: PDB / ID: 6pbg
TitleCrystal structure of WD-repeat domain of human coatomer subunit Alpha (COPA)
ComponentsCoatomer subunit alpha
KeywordsPROTEIN TRANSPORT / COPA / WD-repeat / Coatomer Subunit Alpha / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


pancreatic juice secretion / 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 / hormone activity ...pancreatic juice secretion / 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 / hormone activity / growth cone / Golgi membrane / endoplasmic reticulum membrane / structural molecule activity / extracellular space / extracellular exosome / membrane / cytosol / cytoplasm
Similarity search - Function
: / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / Coatomer (COPI) alpha subunit C-terminus / : / Coatomer, WD associated region / Coatomer WD associated region / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Anaphase-promoting complex subunit 4 WD40 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 / Coatomer WD associated region / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Anaphase-promoting complex subunit 4 WD40 domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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. / 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
L(+)-TARTARIC ACID / Coatomer subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsHalabelian, L. / Zeng, H. / Dong, A. / Loppnau, P. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of W repeat domain of human coatomer subunit Alpha (COPA)
Authors: Halabelian, L. / Zeng, H. / Dong, A. / Loppnau, P. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
History
DepositionJun 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2213
Polymers37,0711
Non-polymers1502
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.633, 85.452, 47.913
Angle α, β, γ (deg.)90.000, 107.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Coatomer subunit alpha / Alpha-coat protein / Alpha-COP / HEP-COP / HEPCOP


Mass: 37071.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPA / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53621
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.83 Å3/Da / Density % sol: 32.73 % / Mosaicity: 0.948 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M di-Ammonium Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 26521 / % possible obs: 93.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.096 / Χ2: 1.209 / Net I/σ(I): 8.3 / Num. measured all: 170533
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.72-1.754.10.4729770.8330.2360.5320.89969.3
1.75-1.784.60.51910670.8330.2530.5810.86376.2
1.78-1.824.90.47911940.8890.2260.5320.83984.1
1.82-1.855.20.41113070.930.1930.4560.85892.8
1.85-1.895.70.36313080.9420.1630.40.90593.7
1.89-1.9460.3113460.9570.1360.3390.95794.1
1.94-1.996.30.26913450.9740.1150.293196.3
1.99-2.046.60.2413150.9820.1010.2611.04692
2.04-2.16.50.20713540.9840.0860.2241.13596.4
2.1-2.176.70.19113440.9850.0790.2071.18694
2.17-2.246.70.16613640.9890.0680.181.14198
2.24-2.336.80.15513510.9870.0640.1681.16396.2
2.33-2.446.90.14313890.9910.0580.1551.08798.4
2.44-2.577.10.13413900.9910.0540.1451.16197.7
2.57-2.737.20.10613850.9950.0420.1141.14298.2
2.73-2.947.30.08614040.9970.0340.0931.15298.5
2.94-3.247.40.06414010.9980.0250.0691.37199.2
3.24-3.717.30.05214270.9980.0210.0561.71999.5
3.71-4.677.20.04514200.9990.0180.0491.8899.6
4.67-506.60.04314330.9990.0180.0471.73997.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.72 Å20.75 Å
Translation1.72 Å20.75 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J87

4j87


Resolution: 1.72→20.76 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.875 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.126
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 740 2.8 %RANDOM
Rwork0.1714 ---
obs0.1727 25722 93.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.72 Å2 / Biso mean: 17.7 Å2 / Biso min: 10.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å2-0.03 Å2
2--1.89 Å20 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.72→20.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 11 220 2689
Biso mean--23.54 27.17 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132578
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172302
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.6373508
X-RAY DIFFRACTIONr_angle_other_deg1.2581.585321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1695311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06221.233146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60615417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4221519
X-RAY DIFFRACTIONr_chiral_restr0.0640.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
LS refinement shellResolution: 1.72→1.765 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 54 -
Rwork0.264 1414 -
all-1468 -
obs--70.71 %

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