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- PDB-3odt: Crystal structure of WD40 beta propeller domain of Doa1 -

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Basic information

Entry
Database: PDB / ID: 3odt
TitleCrystal structure of WD40 beta propeller domain of Doa1
ComponentsProtein DOA1
KeywordsNUCLEAR PROTEIN / Ubiquitin
Function / homology
Function and homology information


ribophagy / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin recycling / cytoplasmic side of mitochondrial outer membrane / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-modified protein reader activity / ubiquitin binding / double-strand break repair via nonhomologous end joining / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane ...ribophagy / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin recycling / cytoplasmic side of mitochondrial outer membrane / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-modified protein reader activity / ubiquitin binding / double-strand break repair via nonhomologous end joining / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein-containing complex binding / nucleus / cytoplasm
Similarity search - Function
PUL domain / PLAA family ubiquitin binding domain / PFU domain superfamily / PUL domain / PFU (PLAA family ubiquitin binding) / PFU domain profile. / PUL domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...PUL domain / PLAA family ubiquitin binding domain / PFU domain superfamily / PUL domain / PFU (PLAA family ubiquitin binding) / PFU domain profile. / PUL domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Armadillo-type fold / G-protein beta WD-40 repeat / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsPashkova, N. / Gakhar, L. / Winistorfer, S.C. / Yu, L. / Ramaswamy, S. / Piper, R.C.
CitationJournal: Mol.Cell / Year: 2010
Title: WD40 Repeat Propellers Define a Ubiquitin-Binding Domain that Regulates Turnover of F Box Proteins.
Authors: Pashkova, N. / Gakhar, L. / Winistorfer, S.C. / Yu, L. / Ramaswamy, S. / Piper, R.C.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein DOA1
B: Protein DOA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5847
Polymers69,2292
Non-polymers3565
Water18,5191028
1
A: Protein DOA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8904
Polymers34,6141
Non-polymers2753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein DOA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6953
Polymers34,6141
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.656, 87.996, 92.265
Angle α, β, γ (deg.)90.00, 96.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein DOA1


Mass: 34614.367 Da / Num. of mol.: 2 / Fragment: WD40 beta propeller domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DOA1, UFD3, ZZZ4, YKL213C / Production host: Escherichia coli (E. coli) / References: UniProt: P36037
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1028 / Source method: isolated from a natural source / Formula: H2O

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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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 0.1 M CaCl2, 15% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97864,0.97880, 0.96411
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 1, 2008
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978641
20.97881
30.964111
ReflectionResolution: 1.35→29.33 Å / Num. all: 107515 / Num. obs: 107515 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.24 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.1
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.64 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 3.3 / % possible all: 67.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.35→28.854 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.176 5390 5.02 %RANDOM
Rwork0.1364 ---
obs0.1385 107429 91.99 %-
all-107429 --
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.605 Å2 / ksol: 0.423 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1239 Å2-0 Å2-0.3932 Å2
2---0.2131 Å20 Å2
3---0.0892 Å2
Refinement stepCycle: LAST / Resolution: 1.35→28.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 16 1028 5640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124781
X-RAY DIFFRACTIONf_angle_d1.396493
X-RAY DIFFRACTIONf_dihedral_angle_d12.7191696
X-RAY DIFFRACTIONf_chiral_restr0.084736
X-RAY DIFFRACTIONf_plane_restr0.007823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.39830.33873810.25557538X-RAY DIFFRACTION68
1.3983-1.45430.30715200.22649587X-RAY DIFFRACTION87
1.4543-1.52050.23585110.159310115X-RAY DIFFRACTION91
1.5205-1.60060.21145380.133210145X-RAY DIFFRACTION92
1.6006-1.70090.1895740.122410292X-RAY DIFFRACTION94
1.7009-1.83220.18985740.123910530X-RAY DIFFRACTION95
1.8322-2.01650.17435680.129710816X-RAY DIFFRACTION97
2.0165-2.30820.16375740.125110887X-RAY DIFFRACTION98
2.3082-2.90770.15955830.132810981X-RAY DIFFRACTION99
2.9077-28.86090.13925670.128911148X-RAY DIFFRACTION99

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