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- PDB-9r6v: Crystal structure of the DOC domain of the E3 ligase HECTD3 -

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Basic information

Entry
Database: PDB / ID: 9r6v
TitleCrystal structure of the DOC domain of the E3 ligase HECTD3
ComponentsE3 ubiquitin-protein ligase HECTD3
KeywordsLIGASE / E3-ligase / ubiquitin / ubiquitination / HECT-ligase
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / syntaxin binding / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / perinuclear region of cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase HECTD3 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HECTD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsEsposito, D. / Huber, J. / Maslen, S. / Rittinger, K.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2075, CC2000 United Kingdom
UK Research and Innovation (UKRI)CC2075, CC2000 United Kingdom
Cancer Research UKCC2075, CC2000 United Kingdom
Wellcome TrustCC2075, CC2000 United Kingdom
CitationJournal: To Be Published
Title: Structural mechanism of the minimal ligase HECTD3
Authors: Huber, J. / Esposito, D. / Maslen, S. / Rittinger, K.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HECTD3
B: E3 ubiquitin-protein ligase HECTD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1754
Polymers32,1262
Non-polymers492
Water3,153175
1
A: E3 ubiquitin-protein ligase HECTD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0872
Polymers16,0631
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase HECTD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0872
Polymers16,0631
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.822, 52.640, 115.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein E3 ubiquitin-protein ligase HECTD3 / HECT domain-containing protein 3 / HECT-type E3 ubiquitin transferase HECTD3


Mass: 16063.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal GPG residues are residual from the 3C-protease cleavage sequence.
Source: (gene. exp.) Homo sapiens (human) / Gene: HECTD3 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q5T447, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HECTD3 DOC domain is in 50 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP at a concentration of 13.5 mg/ml. Crystals grew from a 100 nL protein solution plus 100 nL reservoir made of 0.1 M HEPES ...Details: HECTD3 DOC domain is in 50 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP at a concentration of 13.5 mg/ml. Crystals grew from a 100 nL protein solution plus 100 nL reservoir made of 0.1 M HEPES pH 7.5, 30% (w/v) PEG 400, 5% PEG 3000 and 10% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.61→38.85 Å / Num. obs: 40411 / % possible obs: 99.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.54 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.7
Reflection shellResolution: 1.61→1.65 Å / Num. unique obs: 2852 / CC1/2: 0.455

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→38.85 Å / SU ML: 0.1907 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2124 1930 5.06 %
Rwork0.1951 36225 -
obs0.196 38155 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.07 Å2
Refinement stepCycle: LAST / Resolution: 1.61→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 2 175 2339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572190
X-RAY DIFFRACTIONf_angle_d0.76582962
X-RAY DIFFRACTIONf_chiral_restr0.0536352
X-RAY DIFFRACTIONf_plane_restr0.0086376
X-RAY DIFFRACTIONf_dihedral_angle_d15.6717818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.32531170.29972604X-RAY DIFFRACTION99.6
1.65-1.690.31371260.27782539X-RAY DIFFRACTION99.51
1.69-1.740.25321220.24912557X-RAY DIFFRACTION99.37
1.74-1.80.24891340.24142549X-RAY DIFFRACTION99.37
1.8-1.870.22181390.22272581X-RAY DIFFRACTION99.52
1.87-1.940.26681360.21982548X-RAY DIFFRACTION99.22
1.94-2.030.25291630.21452561X-RAY DIFFRACTION99.89
2.03-2.140.24591340.18832561X-RAY DIFFRACTION99.56
2.14-2.270.22221430.18772524X-RAY DIFFRACTION96.53
2.27-2.440.20391310.18422581X-RAY DIFFRACTION99.27
2.44-2.690.21091570.1882603X-RAY DIFFRACTION99.93
2.69-3.080.20771420.19372627X-RAY DIFFRACTION99.93
3.08-3.880.19761300.17272668X-RAY DIFFRACTION99.5
3.88-38.850.17161560.18112722X-RAY DIFFRACTION97.46

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