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- PDB-5o75: Ube4B U-box domain -

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Basic information

Entry
Database: PDB / ID: 5o75
TitleUbe4B U-box domain
ComponentsUbiquitin conjugation factor E4 B
KeywordsLIGASE / E3 U-box / ubiquitin transfer
Function / homology
Function and homology information


granzyme-mediated apoptotic signaling pathway / ubiquitin-ubiquitin ligase activity / response to UV / ubiquitin ligase complex / ERAD pathway / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / enzyme binding ...granzyme-mediated apoptotic signaling pathway / ubiquitin-ubiquitin ligase activity / response to UV / ubiquitin ligase complex / ERAD pathway / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / enzyme binding / nucleus / cytoplasm
Similarity search - Function
Ubiquitin conjugation factor E4, core / Ubiquitin conjugation factor E4 / Ubiquitin elongating factor core / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type ...Ubiquitin conjugation factor E4, core / Ubiquitin conjugation factor E4 / Ubiquitin elongating factor core / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin conjugation factor E4 B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.483 Å
AuthorsGabrielsen, M. / Buetow, L. / Nakasone, M.A. / Huang, D.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC596/A23278 United Kingdom
European Research Council647849 United Kingdom
CitationJournal: Mol. Cell / Year: 2017
Title: A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants.
Authors: Gabrielsen, M. / Buetow, L. / Nakasone, M.A. / Ahmed, S.F. / Sibbet, G.J. / Smith, B.O. / Zhang, W. / Sidhu, S.S. / Huang, D.T.
History
DepositionJun 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jan 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin conjugation factor E4 B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1102
Polymers9,0141
Non-polymers961
Water79344
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area4940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.180, 80.180, 39.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-1315-

HOH

21A-1332-

HOH

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Components

#1: Protein Ubiquitin conjugation factor E4 B / Homozygously deleted in neuroblastoma 1 / RING-type E3 ubiquitin transferase E4 B / Ubiquitin ...Homozygously deleted in neuroblastoma 1 / RING-type E3 ubiquitin transferase E4 B / Ubiquitin fusion degradation protein 2


Mass: 9014.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE4B, HDNB1, KIAA0684, UFD2 / Plasmid: pGEX4T.1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O95155, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M citric acid, pH 5.5, 1.9 M ammonium sulphate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.483→69.438 Å / Num. obs: 11868 / % possible obs: 91.9 % / Redundancy: 17 % / Biso Wilson estimate: 25.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.015 / Net I/σ(I): 27.9
Reflection shellResolution: 1.483→1.509 Å / Redundancy: 15 % / Rmerge(I) obs: 1.194 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 636 / CC1/2: 0.771 / Rpim(I) all: 0.435 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L1Z

3l1z


Resolution: 1.483→40.09 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.04
RfactorNum. reflection% reflection
Rfree0.224 581 4.9 %
Rwork0.1954 --
obs0.1966 11866 91.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.46 Å2
Refinement stepCycle: LAST / Resolution: 1.483→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms577 0 5 44 626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008612
X-RAY DIFFRACTIONf_angle_d1.029834
X-RAY DIFFRACTIONf_dihedral_angle_d18.112405
X-RAY DIFFRACTIONf_chiral_restr0.08993
X-RAY DIFFRACTIONf_plane_restr0.007111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.483-1.63230.32891570.26282989X-RAY DIFFRACTION100
1.6323-1.86850.28031510.24192850X-RAY DIFFRACTION95
1.8685-2.35410.24481240.23362365X-RAY DIFFRACTION77
2.3541-40.10460.20181490.17663081X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 14.0621 Å / Origin y: 41.9737 Å / Origin z: 88.9428 Å
111213212223313233
T0.2163 Å2-0.028 Å20.0254 Å2-0.3023 Å2-0.0261 Å2--0.1991 Å2
L3.3824 °20.4783 °20.4802 °2-4.8548 °2-1.4051 °2--3.635 °2
S0.1073 Å °-0.0765 Å °0.2371 Å °0.254 Å °-0.2308 Å °-0.0567 Å °-0.3888 Å °0.4249 Å °0.0884 Å °
Refinement TLS groupSelection details: all

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