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- PDB-5tdb: Crystal structure of the human UBR-box domain from UBR2 in comple... -

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Basic information

Entry
Database: PDB / ID: 5tdb
TitleCrystal structure of the human UBR-box domain from UBR2 in complex with asymmetrically double methylated arginine peptide
Components
  • DA2-ILE-PHE-SER peptide
  • E3 ubiquitin-protein ligase UBR2
KeywordsLIGASE / UBR-box / N-end rule / asymmetrically double methylated arginine / ADMA
Function / homology
Function and homology information


L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / histone ubiquitin ligase activity / male meiotic nuclear division / retrotransposon silencing / cellular response to L-leucine / negative regulation of TOR signaling / reciprocal meiotic recombination / male meiosis I / ubiquitin ligase complex ...L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / histone ubiquitin ligase activity / male meiotic nuclear division / retrotransposon silencing / cellular response to L-leucine / negative regulation of TOR signaling / reciprocal meiotic recombination / male meiosis I / ubiquitin ligase complex / heterochromatin formation / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / spermatogenesis / 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 / 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. ...: / E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / Proteolysis_6 C-terminal / 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 / Resolution: 1.101 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 2.0Jan 8, 2020Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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: DA2-ILE-PHE-SER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1586
Polymers8,9002
Non-polymers2584
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-6 kcal/mol
Surface area4250 Å2
Unit cell
Length a, b, c (Å)29.573, 37.168, 29.746
Angle α, β, γ (deg.)90.00, 109.50, 90.00
Int Tables number4
Space group name H-MP1211

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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 DA2-ILE-PHE-SER peptide


Mass: 549.663 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.73 Å3/Da / Density % sol: 28.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 and 25% PEG 3350

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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: 1.1→15.463 Å / Num. obs: 24588 / % possible obs: 99.46 % / Redundancy: 4.1 % / Net I/σ(I): 32.6
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.03 / CC1/2: 0.815 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.101→15.463 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.134 1166 4.74 %
Rwork0.1248 --
obs0.1252 24587 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.101→15.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms558 0 7 54 619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007584
X-RAY DIFFRACTIONf_angle_d1.038785
X-RAY DIFFRACTIONf_dihedral_angle_d16.668215
X-RAY DIFFRACTIONf_chiral_restr0.07279
X-RAY DIFFRACTIONf_plane_restr0.006103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1005-1.15060.19221540.18072798X-RAY DIFFRACTION97
1.1506-1.21120.16771360.14972939X-RAY DIFFRACTION100
1.2112-1.28710.15631350.13632950X-RAY DIFFRACTION100
1.2871-1.38640.1421500.11912924X-RAY DIFFRACTION100
1.3864-1.52580.14941540.10682929X-RAY DIFFRACTION100
1.5258-1.74630.09831710.09582934X-RAY DIFFRACTION100
1.7463-2.19920.12541400.11782957X-RAY DIFFRACTION100
2.1992-15.46460.13531260.13232990X-RAY DIFFRACTION99

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