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- PDB-6loh: Crystal structure of the catalytic domain of human ubiquitin liga... -

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Basic information

Entry
Database: PDB / ID: 6loh
TitleCrystal structure of the catalytic domain of human ubiquitin ligase AREL1
ComponentsApoptosis-resistant E3 ubiquitin protein ligase 1
KeywordsLIGASE / AREL1 / ubiquitin ligase / HECT
Function / homology
Function and homology information


protein K33-linked ubiquitination / HECT-type E3 ubiquitin transferase / protein K11-linked ubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of inflammatory response / ubiquitin-dependent protein catabolic process / protein ubiquitination / apoptotic process ...protein K33-linked ubiquitination / HECT-type E3 ubiquitin transferase / protein K11-linked ubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of inflammatory response / ubiquitin-dependent protein catabolic process / protein ubiquitination / apoptotic process / negative regulation of apoptotic process / cytosol / cytoplasm
Similarity search - Function
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / : / HECT domain / HECT, E3 ligase catalytic domain ...Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Apoptosis-resistant E3 ubiquitin protein ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.207 Å
AuthorsChen, Z.Z. / Li, Z.H. / Shang, G.H.
CitationJournal: Prog.Biochem.Biophys. / Year: 2020
Title: Crystal structure of the catalytic domain of human ubiquitin ligase AREL1
Authors: Li, Z.H. / Shang, G.H. / Tang, C.J. / Tian, Z.Z. / Wu, W. / Chen, Z.Z.
History
DepositionJan 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: Apoptosis-resistant E3 ubiquitin protein ligase 1
B: Apoptosis-resistant E3 ubiquitin protein ligase 1
C: Apoptosis-resistant E3 ubiquitin protein ligase 1


Theoretical massNumber of molelcules
Total (without water)135,0843
Polymers135,0843
Non-polymers00
Water1086
1
A: Apoptosis-resistant E3 ubiquitin protein ligase 1

A: Apoptosis-resistant E3 ubiquitin protein ligase 1


Theoretical massNumber of molelcules
Total (without water)90,0562
Polymers90,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area2430 Å2
ΔGint-18 kcal/mol
Surface area33210 Å2
MethodPISA
2
B: Apoptosis-resistant E3 ubiquitin protein ligase 1
C: Apoptosis-resistant E3 ubiquitin protein ligase 1


Theoretical massNumber of molelcules
Total (without water)90,0562
Polymers90,0562
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-17 kcal/mol
Surface area33950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.231, 150.231, 342.645
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 45028.156 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.: 6 / 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: 4.13 Å3/Da / Density % sol: 70.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.4
Details: 0.1M Sodium phosphate pH 6.4, 0.2M Potassium chloride, 2.25M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.207→50 Å / Num. obs: 38276 / % possible obs: 98 % / Redundancy: 3.4 % / CC1/2: 0.979 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.071 / Rrim(I) all: 0.141 / Net I/σ(I): 9.6
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 1756 / CC1/2: 0.635 / CC star: 0.881 / Rpim(I) all: 0.381 / Rrim(I) all: 0.742 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.207→49.223 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.92 / SU B: 16.439 / SU ML: 0.266 / Cross valid method: FREE R-VALUE / ESU R: 1.2 / ESU R Free: 0.365
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2249 1878 4.906 %
Rwork0.2108 36398 -
all0.211 --
obs-38276 99.83 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 68.887 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.065 Å2
Refinement stepCycle: LAST / Resolution: 3.207→49.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8984 0 0 6 8990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139198
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178577
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0840.0114563
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.63912437
X-RAY DIFFRACTIONr_angle_other_deg1.3031.57419693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53651113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97822.264508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.813151568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.331557
X-RAY DIFFRACTIONr_chiral_restr0.0850.21150
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022273
X-RAY DIFFRACTIONr_nbd_refined0.2310.21968
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.28050
X-RAY DIFFRACTIONr_nbtor_refined0.180.24361
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.24656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2153
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3640.222
X-RAY DIFFRACTIONr_nbd_other0.160.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3130.21
X-RAY DIFFRACTIONr_mcbond_it4.1897.2554473
X-RAY DIFFRACTIONr_mcbond_other4.1817.2564472
X-RAY DIFFRACTIONr_mcangle_it6.91210.8695579
X-RAY DIFFRACTIONr_mcangle_other6.91210.875580
X-RAY DIFFRACTIONr_scbond_it4.1237.5984725
X-RAY DIFFRACTIONr_scbond_other4.1237.5984726
X-RAY DIFFRACTIONr_scangle_it6.96111.2346858
X-RAY DIFFRACTIONr_scangle_other6.96111.2346859
X-RAY DIFFRACTIONr_lrange_it10.216144.48919933
X-RAY DIFFRACTIONr_lrange_other10.216144.48919934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.207-3.290.3151410.2952572X-RAY DIFFRACTION98.3684
3.29-3.380.3011470.2812531X-RAY DIFFRACTION100
3.38-3.4770.2621160.2512524X-RAY DIFFRACTION100
3.477-3.5840.269970.2442464X-RAY DIFFRACTION100
3.584-3.7010.2891320.2372332X-RAY DIFFRACTION100
3.701-3.830.2441160.2252287X-RAY DIFFRACTION100
3.83-3.9730.221070.2192212X-RAY DIFFRACTION100
3.973-4.1350.2251000.1952139X-RAY DIFFRACTION100
4.135-4.3170.2011160.1752026X-RAY DIFFRACTION100
4.317-4.5260.1861060.1681972X-RAY DIFFRACTION100
4.526-4.7690.176970.1671870X-RAY DIFFRACTION100
4.769-5.0550.1821120.1731771X-RAY DIFFRACTION100
5.055-5.40.198810.1811685X-RAY DIFFRACTION100
5.4-5.8270.206920.1821576X-RAY DIFFRACTION100
5.827-6.3750.28740.2061455X-RAY DIFFRACTION100
6.375-7.1130.243680.2071346X-RAY DIFFRACTION100
7.113-8.1860.217580.1841202X-RAY DIFFRACTION100
8.186-9.9590.237470.1891047X-RAY DIFFRACTION100
9.959-13.8130.181510.175834X-RAY DIFFRACTION100
13.813-490.245200.439553X-RAY DIFFRACTION99.8258

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