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- PDB-6jx5: Hect domain of AREL1 -

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Basic information

Entry
Database: PDB / ID: 6jx5
TitleHect domain of AREL1
ComponentsApoptosis-resistant E3 ubiquitin protein ligase 1
KeywordsAPOPTOSIS / HECT domain
Function / homology
Function and homology information


protein K33-linked ubiquitination / protein K11-linked ubiquitination / HECT-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of inflammatory response / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...protein K33-linked ubiquitination / protein K11-linked ubiquitination / HECT-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of inflammatory response / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / apoptotic process / negative regulation of apoptotic process / cytosol / cytoplasm
Similarity search - Function
Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Apoptosis-resistant E3 ubiquitin protein ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsSivaraman, J. / Singh, S. / Ng, J. / Nayak, D.
Funding support Singapore, 2items
OrganizationGrant numberCountry
Ministry of Education (Singapore)R-154-000-B03-112 Singapore
Ministry of Education (Singapore)R154-000-A72-114 Singapore
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural insights into a HECT-type E3 ligase AREL1 and its ubiquitination activitiesin vitro.
Authors: Singh, S. / Ng, J. / Nayak, D. / Sivaraman, J.
History
DepositionApr 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
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
C: Apoptosis-resistant E3 ubiquitin protein ligase 1
A: Apoptosis-resistant E3 ubiquitin protein ligase 1
B: Apoptosis-resistant E3 ubiquitin protein ligase 1


Theoretical massNumber of molelcules
Total (without water)133,6283
Polymers133,6283
Non-polymers00
Water6,593366
1
C: Apoptosis-resistant E3 ubiquitin protein ligase 1


Theoretical massNumber of molelcules
Total (without water)44,5431
Polymers44,5431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Apoptosis-resistant E3 ubiquitin protein ligase 1


Theoretical massNumber of molelcules
Total (without water)44,5431
Polymers44,5431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Apoptosis-resistant E3 ubiquitin protein ligase 1


Theoretical massNumber of molelcules
Total (without water)44,5431
Polymers44,5431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.156, 121.057, 80.798
Angle α, β, γ (deg.)90.00, 91.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1019-

HOH

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Components

#1: Protein Apoptosis-resistant E3 ubiquitin protein ligase 1 / Apoptosis-resistant HECT-type E3 ubiquitin transferase 1


Mass: 44542.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AREL1, KIAA0317 / Production host: Escherichia coli (E. coli)
References: UniProt: O15033, HECT-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion / Details: 100mM Bis Tris (pH 5.5), 200mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 296 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9926 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9926 Å / Relative weight: 1
ReflectionResolution: 2.4→47.86 Å / Num. obs: 77372 / % possible obs: 98.65 % / Redundancy: 5.7 % / Biso Wilson estimate: 36.23 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.049 / Net I/σ(I): 19.22
Reflection shellResolution: 2.402→2.488 Å / Num. unique obs: 7296 / CC1/2: 0.832 / Rpim(I) all: 0.235

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TUG

3tug


Resolution: 2.402→47.86 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.68
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 3742 4.84 %RANDOM
Rwork0.1857 ---
obs0.1873 77372 98.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.402→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9146 0 0 366 9512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039408
X-RAY DIFFRACTIONf_angle_d0.62712726
X-RAY DIFFRACTIONf_dihedral_angle_d4.7145607
X-RAY DIFFRACTIONf_chiral_restr0.0421386
X-RAY DIFFRACTIONf_plane_restr0.0041638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4021-2.43250.32751320.24622455X-RAY DIFFRACTION89
2.4325-2.46450.3041530.22732634X-RAY DIFFRACTION96
2.4645-2.49820.27851580.22982589X-RAY DIFFRACTION97
2.4982-2.53390.28831280.22122755X-RAY DIFFRACTION98
2.5339-2.57180.28461240.21642722X-RAY DIFFRACTION99
2.5718-2.61190.2531360.21372714X-RAY DIFFRACTION98
2.6119-2.65480.26571310.2022708X-RAY DIFFRACTION99
2.6548-2.70050.24071320.20072735X-RAY DIFFRACTION99
2.7005-2.74960.23461500.20012720X-RAY DIFFRACTION99
2.7496-2.80250.23691560.20282706X-RAY DIFFRACTION99
2.8025-2.85970.25611260.21162748X-RAY DIFFRACTION99
2.8597-2.92190.26831310.21942724X-RAY DIFFRACTION99
2.9219-2.98990.25221120.20952786X-RAY DIFFRACTION99
2.9899-3.06460.25131680.20752684X-RAY DIFFRACTION99
3.0646-3.14750.22561560.19922717X-RAY DIFFRACTION99
3.1475-3.24010.22961660.20512716X-RAY DIFFRACTION99
3.2401-3.34460.28251270.19412776X-RAY DIFFRACTION99
3.3446-3.46410.24571250.19612760X-RAY DIFFRACTION99
3.4641-3.60280.21511290.19352744X-RAY DIFFRACTION99
3.6028-3.76670.2199900.18462834X-RAY DIFFRACTION100
3.7667-3.96520.17441180.17662734X-RAY DIFFRACTION100
3.9652-4.21350.22511300.1622790X-RAY DIFFRACTION100
4.2135-4.53860.16421620.14452738X-RAY DIFFRACTION100
4.5386-4.99490.19091640.15692747X-RAY DIFFRACTION100
4.9949-5.71670.19161490.17432781X-RAY DIFFRACTION100
5.7167-7.19860.1921410.1852787X-RAY DIFFRACTION100
7.1986-48.44690.1561480.15622826X-RAY DIFFRACTION100

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