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- PDB-5um3: Crystal structure of the V122L mutant of human UBR-box domain fro... -

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Basic information

Entry
Database: PDB / ID: 5um3
TitleCrystal structure of the V122L mutant of human UBR-box domain from UBR2
ComponentsE3 ubiquitin-protein ligase UBR2
KeywordsLIGASE / UBR-box domain / johansson blizard / zinc finger / N-end rule
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: 1.198 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
DepositionJan 26, 2017Deposition 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 / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4484
Polymers8,2511
Non-polymers1963
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.177, 29.375, 66.052
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 / RING-type E3 ubiquitin transferase UBR2 / Ubiquitin-protein ligase E3-alpha-2 / ...N-recognin-2 / RING-type E3 ubiquitin transferase UBR2 / Ubiquitin-protein ligase E3-alpha-2 / Ubiquitin-protein ligase E3-alpha-II


Mass: 8251.384 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, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 92 / 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: 28.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6263 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6263 Å / Relative weight: 1
ReflectionResolution: 1.198→17.62 Å / Num. obs: 18167 / % possible obs: 98.1 % / Redundancy: 7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.09856 / Rpim(I) all: 0.03891 / Net I/σ(I): 17.87
Reflection shellResolution: 1.198→1.241 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 1580 / CC1/2: 0.747 / Rpim(I) all: 0.3284 / % possible all: 86.43

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TDD

5tdd


Resolution: 1.198→17.618 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.43
RfactorNum. reflection% reflection
Rfree0.1583 1816 10 %
Rwork0.1369 --
obs0.139 18153 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.198→17.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms546 0 3 92 641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006590
X-RAY DIFFRACTIONf_angle_d0.953798
X-RAY DIFFRACTIONf_dihedral_angle_d12.22221
X-RAY DIFFRACTIONf_chiral_restr0.0778
X-RAY DIFFRACTIONf_plane_restr0.006109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1985-1.23090.29171160.23771063X-RAY DIFFRACTION84
1.2309-1.26710.21341320.2041195X-RAY DIFFRACTION94
1.2671-1.3080.20741400.17261230X-RAY DIFFRACTION99
1.308-1.35470.24061360.15491249X-RAY DIFFRACTION100
1.3547-1.40890.15531420.13061264X-RAY DIFFRACTION100
1.4089-1.4730.16421430.12161280X-RAY DIFFRACTION100
1.473-1.55060.14641430.10621249X-RAY DIFFRACTION100
1.5506-1.64770.13471400.1011269X-RAY DIFFRACTION100
1.6477-1.77480.12431390.10631271X-RAY DIFFRACTION100
1.7748-1.95330.14661480.1171292X-RAY DIFFRACTION100
1.9533-2.23540.14431400.11591287X-RAY DIFFRACTION100
2.2354-2.81450.13841420.14061313X-RAY DIFFRACTION100
2.8145-17.61980.16931550.15451375X-RAY DIFFRACTION99

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