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- PDB-7us1: Structure of parkin (R0RB) bound to two phospho-ubiquitin molecules -

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Basic information

Entry
Database: PDB / ID: 7us1
TitleStructure of parkin (R0RB) bound to two phospho-ubiquitin molecules
Components
  • E3 ubiquitin-protein ligase parkin
  • Ubiquitin-G76 deletion
KeywordsLIGASE / Parkin R0RB / R0RB:2pUb / R0RB:pUb
Function / homology
Function and homology information


RBR-type E3 ubiquitin transferase / ubiquitin ligase complex / autophagy / ubiquitin-protein transferase activity / protein ubiquitination / mitochondrion / zinc ion binding / cytosol
Similarity search - Function
E3 ubiquitin ligase RBR family / E3 ubiquitin-protein ligase parkin / RING/Ubox-like zinc-binding domain / Parkin, RING/Ubox like zinc-binding domain / : / : / : / RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / IBR domain ...E3 ubiquitin ligase RBR family / E3 ubiquitin-protein ligase parkin / RING/Ubox-like zinc-binding domain / Parkin, RING/Ubox like zinc-binding domain / : / : / : / RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Ubiquitin B / E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.484 Å
AuthorsFakih, R. / Sauve, V. / Gehring, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Michael J. Fox Foundation United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structure of the second phosphoubiquitin-binding site in parkin.
Authors: Fakih, R. / Sauve, V. / Gehring, K.
History
DepositionApr 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase parkin
B: Ubiquitin-G76 deletion
C: Ubiquitin-G76 deletion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,23814
Polymers43,4923
Non-polymers74711
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.078, 83.078, 253.816
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein E3 ubiquitin-protein ligase parkin


Mass: 26406.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Park2 / Production host: Escherichia coli (E. coli)
References: UniProt: S4X0T1, RBR-type E3 ubiquitin transferase
#2: Protein Ubiquitin-G76 deletion


Mass: 8542.706 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39

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Non-polymers , 4 types, 50 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Bis-Tris propane pH 7.5, 20.5% PEG3350, 0.2M NaI

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1808 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 2.484→47.59 Å / Num. obs: 19185 / % possible obs: 99.9 % / Redundancy: 18.3 % / CC1/2: 0.999 / Net I/σ(I): 21.08
Reflection shellResolution: 2.484→2.573 Å / Num. unique obs: 1847 / CC1/2: 0.523

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata scaling
PHENIXphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GLC

6glc


Resolution: 2.484→47.59 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 947 4.94 %
Rwork0.2294 18234 -
obs0.2309 19181 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.25 Å2 / Biso mean: 77.6442 Å2 / Biso min: 41.4 Å2
Refinement stepCycle: final / Resolution: 2.484→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 29 39 3079
Biso mean--70.86 68.25 -
Num. residues----386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.484-2.620.36211380.3284251399
2.62-2.780.3561310.30282547100
2.78-2.990.40891150.32622553100
2.99-3.290.33231280.27852578100
3.3-3.770.30121510.2572576100
3.77-4.750.23111270.19012633100
4.75-47.590.19561570.19492834100
Refinement TLS params.Method: refined / Origin x: -25.6556 Å / Origin y: 31.6822 Å / Origin z: -21.745 Å
111213212223313233
T0.4233 Å2-0.0988 Å20.0184 Å2-0.3863 Å2-0.0956 Å2--0.5149 Å2
L2.1584 °20.5222 °21.045 °2-1.1342 °2-0.408 °2--3.773 °2
S0.1714 Å °-0.1119 Å °0.237 Å °0.2087 Å °-0.1533 Å °0.1845 Å °-0.1319 Å °0.2939 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA140 - 379
2X-RAY DIFFRACTION1allA501 - 506
3X-RAY DIFFRACTION1allE1 - 5
4X-RAY DIFFRACTION1allB1 - 74
5X-RAY DIFFRACTION1allC1 - 72
6X-RAY DIFFRACTION1allD2 - 58

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