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- PDB-6k2c: Extended Hect domain of UBE3C E3 Ligase -

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Basic information

Entry
Database: PDB / ID: 6k2c
TitleExtended Hect domain of UBE3C E3 Ligase
ComponentsUbiquitin-protein ligase E3C
KeywordsONCOPROTEIN / HECT / E3 ligase / ubiquitination
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / proteasome complex / protein polyubiquitination / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / nucleus
Similarity search - Function
Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / Ubiquitin-protein ligase E3B/C / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. ...Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / Ubiquitin-protein ligase E3B/C / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-protein ligase E3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsSivaraman, J. / Singh, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore)R-154-000-B03-112) and R154-000-A72-114 Singapore
CitationJournal: Biochem.J. / Year: 2020
Title: Crystal structure of HECT domain of UBE3C E3 ligase and its ubiquitination activity.
Authors: Singh, S. / Sivaraman, J.
History
DepositionMay 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Ubiquitin-protein ligase E3C


Theoretical massNumber of molelcules
Total (without water)44,5781
Polymers44,5781
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.610, 75.610, 220.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ubiquitin-protein ligase E3C / HECT-type ubiquitin transferase E3C / HectH2


Mass: 44577.773 Da / Num. of mol.: 1 / Fragment: Hect domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3C, KIAA0010, KIAA10 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15386, HECT-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 296 K / Method: vapor diffusion / Details: 100mM HEPES 7.5, 20% PEG 10000

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Data collection

DiffractionMean temperature: 296 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→48.093 Å / Num. obs: 18388 / % possible obs: 99.9 % / Redundancy: 20.9 % / CC1/2: 0.9923 / Rpim(I) all: 0.036 / Rrim(I) all: 0.169 / Net I/σ(I): 32.45
Reflection shellResolution: 2.7→2.796 Å / Num. unique obs: 1780 / CC1/2: 0.981 / Rpim(I) all: 0.106

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Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ONI

2oni


Resolution: 2.703→48.094 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 867 4.74 %
Rwork0.2373 --
obs0.2392 18279 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.703→48.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 0 23 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082391
X-RAY DIFFRACTIONf_angle_d0.9313225
X-RAY DIFFRACTIONf_dihedral_angle_d3.3181414
X-RAY DIFFRACTIONf_chiral_restr0.049347
X-RAY DIFFRACTIONf_plane_restr0.006419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.703-2.87230.34191430.24672806X-RAY DIFFRACTION99
2.8723-3.0940.28721360.26142832X-RAY DIFFRACTION100
3.094-3.40530.26891570.23862837X-RAY DIFFRACTION100
3.4053-3.89790.25361300.23442894X-RAY DIFFRACTION100
3.8979-4.91020.25451310.21412941X-RAY DIFFRACTION100
4.9102-48.10160.29191700.24863102X-RAY DIFFRACTION100

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