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- PDB-5tda: Crystal structure of the UBR-box domain from UBR2 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5tda
TitleCrystal structure of the UBR-box domain from UBR2 in complex with RLWS N-degron
Components
  • ARG-LEU-TRP-SER peptide
  • E3 ubiquitin-protein ligase UBR2
KeywordsLIGASE / Zn-finger / N-end rule / UBR-box / N-degron
Function / homology
Function and homology information


histone H2A ubiquitin ligase activity / L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / male meiotic nuclear division / transposable element silencing / cellular response to L-leucine / reciprocal meiotic recombination / negative regulation of TOR signaling / positive regulation of T cell receptor signaling pathway / male meiosis I ...histone H2A ubiquitin ligase activity / L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / male meiotic nuclear division / transposable element silencing / cellular response to L-leucine / reciprocal meiotic recombination / negative regulation of TOR signaling / positive regulation of T cell receptor signaling pathway / male meiosis I / protein K63-linked ubiquitination / ubiquitin ligase complex / RING-type E3 ubiquitin transferase / heterochromatin formation / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Zinc finger, UBR-type ...: / E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.79 Å
AuthorsMunoz-Escobar, J. / Kozlov, G. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Citation
Journal: Structure / Year: 2017
Title: Bound Waters Mediate Binding of Diverse Substrates to a Ubiquitin Ligase.
Authors: Munoz-Escobar, J. / Matta-Camacho, E. / Cho, C. / Kozlov, G. / Gehring, K.
#1: Journal: To Be Published
Title: Crystal structure of the UBR-box domain of UBR2 in complex with RLWS N-degron
Authors: Munoz-Escobar, J. / Kozlov, G. / Matta-Camacho, E.P. / Gehring, K.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UBR2
B: ARG-LEU-TRP-SER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1085
Polymers8,9122
Non-polymers1963
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-2 kcal/mol
Surface area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.702, 37.158, 57.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase UBR2 / N-recognin-2 / Ubiquitin-protein ligase E3-alpha-2 / Ubiquitin-protein ligase E3-alpha-II


Mass: 8350.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBR2, C6orf133, KIAA0349 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q8IWV8, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide ARG-LEU-TRP-SER peptide


Mass: 561.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.72 Å3/Da / Density % sol: 28.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5 and 20% PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6362 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6362 Å / Relative weight: 1
ReflectionResolution: 0.79→17.028 Å / Num. obs: 65534 / % possible obs: 96.27 % / Redundancy: 5.4 % / Net I/σ(I): 50.69
Reflection shellResolution: 0.7901→0.8099 Å / Redundancy: 2.6 % / CC1/2: 0.674 / % possible all: 70

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NY3

3ny3


Resolution: 0.79→17.028 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 11.1
RfactorNum. reflection% reflection
Rfree0.1281 2000 3.05 %
Rwork0.1202 --
obs0.1205 65534 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.79→17.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms585 0 3 107 695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009712
X-RAY DIFFRACTIONf_angle_d1.059960
X-RAY DIFFRACTIONf_dihedral_angle_d28.533272
X-RAY DIFFRACTIONf_chiral_restr0.08694
X-RAY DIFFRACTIONf_plane_restr0.008128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.7901-0.80990.28121020.26153250X-RAY DIFFRACTION70
0.8099-0.83180.22531290.22674106X-RAY DIFFRACTION89
0.8318-0.85620.18351450.18564588X-RAY DIFFRACTION98
0.8562-0.88390.1681460.14974652X-RAY DIFFRACTION100
0.8839-0.91550.1351470.1344652X-RAY DIFFRACTION100
0.9155-0.95210.13421470.11454688X-RAY DIFFRACTION100
0.9521-0.99540.09891470.10194661X-RAY DIFFRACTION100
0.9954-1.04790.10791470.09264674X-RAY DIFFRACTION100
1.0479-1.11350.09731480.0914706X-RAY DIFFRACTION100
1.1135-1.19950.09991490.09034737X-RAY DIFFRACTION100
1.1995-1.32020.09081480.09634698X-RAY DIFFRACTION100
1.3202-1.51110.10231500.10524778X-RAY DIFFRACTION100
1.5111-1.90340.11791520.11414795X-RAY DIFFRACTION100
1.9034-17.03190.15941430.13984549X-RAY DIFFRACTION91

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