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- PDB-5tdd: Human UBR-box from UBR2 in complex with HIFS peptide -

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Basic information

Entry
Database: PDB / ID: 5tdd
TitleHuman UBR-box from UBR2 in complex with HIFS peptide
Components
  • E3 ubiquitin-protein ligase UBR2
  • HIS-ILE-PHE-SER peptide
KeywordsLIGASE / UBR-box / N-end rule / Zinc finger / 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 / negative regulation of TOR signaling / reciprocal meiotic recombination / 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 / negative regulation of TOR signaling / reciprocal meiotic recombination / positive regulation of T cell receptor signaling pathway / male meiosis I / protein K63-linked ubiquitination / ubiquitin ligase complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / heterochromatin formation / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin / zinc ion binding / nucleus / cytoplasm / cytosol
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 / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Putative zinc finger in N-recognin (UBR box) ...: / 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 / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Putative zinc finger in N-recognin (UBR box) / 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: 1.55 Å
AuthorsMunoz-Escobar, J. / Kozlov, G. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: 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.
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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UBR2
B: HIS-ILE-PHE-SER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1747
Polymers8,8542
Non-polymers3205
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-2 kcal/mol
Surface area4700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.313, 29.313, 74.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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 / Plasmid: pGEX-6p-1 / 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 HIS-ILE-PHE-SER peptide


Mass: 503.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.8 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 12% PEG 20000

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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: 1.55→20.727 Å / Num. obs: 9083 / % possible obs: 99.94 % / Redundancy: 6.4 % / Rsym value: 0.1 / Net I/σ(I): 32.1
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 4.8 / CC1/2: 0.851 / % possible all: 100

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Processing

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

3ny3


Resolution: 1.55→20.727 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 14.01
RfactorNum. reflection% reflection
Rfree0.1521 913 10.05 %
Rwork0.1059 --
obs0.1106 9083 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→20.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms584 0 11 44 639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01616
X-RAY DIFFRACTIONf_angle_d0.963824
X-RAY DIFFRACTIONf_dihedral_angle_d11.688357
X-RAY DIFFRACTIONf_chiral_restr0.06381
X-RAY DIFFRACTIONf_plane_restr0.008109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5504-1.63210.18651340.09151173X-RAY DIFFRACTION100
1.6321-1.73430.13951310.08351158X-RAY DIFFRACTION100
1.7343-1.86820.15871290.08311149X-RAY DIFFRACTION100
1.8682-2.0560.13561280.0851181X-RAY DIFFRACTION100
2.056-2.35320.13091210.08571165X-RAY DIFFRACTION100
2.3532-2.96340.16161350.11461174X-RAY DIFFRACTION100
2.9634-20.72930.15741350.12961170X-RAY DIFFRACTION100

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