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- PDB-3gae: Crystal Structure of PUL -

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Basic information

Entry
Database: PDB / ID: 3gae
TitleCrystal Structure of PUL
ComponentsProtein DOA1
KeywordsNUCLEAR PROTEIN / Ufd3 / Cdc48 / Armadillo repeat / Nucleus / Phosphoprotein / Ubl conjugation pathway / WD repeat
Function / homology
Function and homology information


ribophagy / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin recycling / cytoplasmic side of mitochondrial outer membrane / 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 ...ribophagy / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin recycling / cytoplasmic side of mitochondrial outer membrane / 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. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical ...PUL domain / PLAA family ubiquitin binding domain / PFU domain superfamily / PUL domain / PFU (PLAA family ubiquitin binding) / PFU domain profile. / PUL domain profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / 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 / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / MAD / Resolution: 1.6 Å
AuthorsZhao, G. / Schindelin, H. / Lennarz, W.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: An Armadillo motif in Ufd3 interacts with Cdc48 and is involved in ubiquitin homeostasis and protein degradation
Authors: Zhao, G. / Li, G. / Schindelin, H. / Lennarz, W.J.
History
DepositionFeb 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,5957
Polymers57,3052
Non-polymers2915
Water9,872548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein DOA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6882
Polymers28,6521
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Protein DOA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9085
Polymers28,6521
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.588, 64.588, 115.798
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Protein DOA1


Mass: 28652.436 Da / Num. of mol.: 2 / Fragment: PUL domain, UNP residues 464-715
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UFD3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36037
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.45 % / Mosaicity: 0.446 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium acetate (pH 5.6), 0.1M MgCl2, 26-28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X26C11
ROTATING ANODERIGAKU RUH3R21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 2, 2008
RIGAKU RAXIS IV++2IMAGE PLATEAug 24, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.54181
ReflectionRedundancy: 4.9 % / Av σ(I) over netI: 22.68 / Number: 135271 / Rmerge(I) obs: 0.074 / Χ2: 1.12 / D res high: 2.15 Å / D res low: 50 Å / Num. obs: 27590 / % possible obs: 96.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.635099.910.0620.9375.7
3.684.6310010.0620.9115.7
3.213.6810010.0711.0735.7
2.923.2110010.0811.1545.6
2.712.9210010.0921.1665.6
2.552.7110010.1091.2315.6
2.422.5510010.1211.2035.4
2.322.4299.910.1351.2973.7
2.232.329210.1561.3462.8
2.152.2372.810.1681.22.4
ReflectionResolution: 1.6→50 Å / Num. all: 71191 / Num. obs: 71191 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.051 / Χ2: 1.081 / Net I/σ(I): 22.68
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7056 / Χ2: 1.074 / % possible all: 98.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.873 / SU B: 3.713 / SU ML: 0.06 / SU R Cruickshank DPI: 0.09 / SU Rfree: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3597 5.1 %RANDOM
Rwork0.179 ---
all0.181 67543 --
obs0.181 71140 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.81 Å2 / Biso mean: 13.473 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å20 Å2
2---0.11 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 15 548 4603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224175
X-RAY DIFFRACTIONr_bond_other_d0.0010.022763
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9655674
X-RAY DIFFRACTIONr_angle_other_deg1.08236810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1525507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9325.816196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50315749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7821514
X-RAY DIFFRACTIONr_chiral_restr0.1120.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02787
X-RAY DIFFRACTIONr_mcbond_it1.0741.52542
X-RAY DIFFRACTIONr_mcbond_other0.3571.51019
X-RAY DIFFRACTIONr_mcangle_it1.78824148
X-RAY DIFFRACTIONr_scbond_it2.66431633
X-RAY DIFFRACTIONr_scangle_it4.1054.51525
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 260 -
Rwork0.242 4878 -
all-5138 -
obs--98.32 %
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)
11.56280.99480.42941.18390.37990.28730.0886-0.0816-0.1166-0.0027-0.0675-0.08870.0107-0.0298-0.02110.09010.0212-0.0080.05940.02840.050756.5158-2.059423.755
21.81740.030.21961.2606-0.08860.6350.0663-0.20870.1016-0.0123-0.0788-0.1166-0.0435-0.03840.01250.0455-0.00680.01310.0833-0.00490.065867.845719.41331.3283
30.5077-0.02680.43491.6594-0.95251.41070.1003-0.0215-0.019-0.1299-0.04410.07730.1960.0244-0.05610.04670.0007-0.02130.07830.01010.054833.2535.507141.3405
41.97890.78540.22741.3783-0.14111.01010.0196-0.08890.2152-0.0205-0.02110.1553-0.07230.00090.00150.04730.00730.00140.0473-0.00160.09139.968328.350735.853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A463 - 651
2X-RAY DIFFRACTION2A652 - 715
3X-RAY DIFFRACTION3B463 - 590
4X-RAY DIFFRACTION4B591 - 715

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