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- PDB-3h1d: Structure of the HUWE1 HECT Domain -

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Basic information

Entry
Database: PDB / ID: 3h1d
TitleStructure of the HUWE1 HECT Domain
ComponentsE3 ubiquitin-protein ligase HUWE1
KeywordsLIGASE / E3Ligase / ubiquitin / HECT / lobe / Alternative splicing / Chromosomal rearrangement / Cytoplasm / Differentiation / Disease mutation / DNA-binding / Mental retardation / Nucleus / Phosphoprotein / Ubl conjugation pathway
Function / homology
Function and homology information


histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / : / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair ...histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / : / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / membrane fusion / cell differentiation / Golgi membrane / Neutrophil degranulation / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) ...Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / WWE domain / UBA-like domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain superfamily / WWE domain / WWE domain profile. / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Armadillo-type fold / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsPartridge, J.R. / Schwartz, T.U.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: A structural element within the HUWE1 HECT domain modulates self-ubiquitination and substrate ubiquitination activities.
Authors: Pandya, R.K. / Partridge, J.R. / Love, K.R. / Schwartz, T.U. / Ploegh, H.L.
History
DepositionApr 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HUWE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8095
Polymers47,4251
Non-polymers3844
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.654, 55.653, 69.585
Angle α, β, γ (deg.)90.00, 122.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase HUWE1


Mass: 47424.609 Da / Num. of mol.: 1 / Fragment: HECT / Mutation: C4099A, C4184A, C4367A
Source method: isolated from a genetically manipulated source
Details: human rhinovirus 3c (HRV3C) protease site / Source: (gene. exp.) Homo sapiens (human) / Gene: HUWE1, KIAA0312, KIAA1578, UREB1, HSPC272 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta cells (Novagen)
References: UniProt: Q7Z6Z7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M citric acid, 1.8 M (NH4)2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.89→30 Å / Num. obs: 30294 / % possible obs: 98.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.072 / Net I/σ(I): 17.2
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.439 / % possible all: 96.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1nd7

1nd7


Resolution: 1.892→29.347 Å / SU ML: 0.68 / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1527 5.04 %
Rwork0.1656 --
obs0.1687 30294 97.75 %
all-30991 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.008 Å2 / ksol: 0.357 e/Å3
Refine analyzeLuzzati coordinate error obs: 0.68 Å
Refinement stepCycle: LAST / Resolution: 1.892→29.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 20 357 3547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113258
X-RAY DIFFRACTIONf_angle_d1.2024391
X-RAY DIFFRACTIONf_dihedral_angle_d15.81200
X-RAY DIFFRACTIONf_chiral_restr0.085460
X-RAY DIFFRACTIONf_plane_restr0.005567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.95310.30721220.23322430X-RAY DIFFRACTION92
1.9531-2.02290.27111650.19382629X-RAY DIFFRACTION99
2.0229-2.10380.26931370.17052625X-RAY DIFFRACTION100
2.1038-2.19960.26061490.17232645X-RAY DIFFRACTION99
2.1996-2.31550.23771200.16962663X-RAY DIFFRACTION99
2.3155-2.46050.25511370.16162656X-RAY DIFFRACTION99
2.4605-2.65040.24131490.16582648X-RAY DIFFRACTION99
2.6504-2.91690.24721340.17452644X-RAY DIFFRACTION99
2.9169-3.33840.20821370.16812638X-RAY DIFFRACTION99
3.3384-4.20410.19371510.14152551X-RAY DIFFRACTION95
4.2041-29.35010.19591260.1522639X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40340.176-0.07510.26540.11780.30110.01190.0471-0.0876-0.06970.00790.05230.0312-0.062-0.01370.08220.0372-0.00790.069-0.00870.0632-7.777625.53739.0372
20.7268-0.0723-0.04220.1146-0.10170.5222-0.1307-0.01790.16860.0791-0.0214-0.0260.00930.06110.08790.1380.0122-0.02640.0885-0.00070.0805-0.97438.309918.1191
30.3943-0.08020.20880.1585-0.09220.13070.0045-0.0108-0.0180.02950.0064-0.0328-0.019-0.0374-0.00660.0330.01910.00760.0112-0.00190.02512.497527.658925.8683
41.9189-0.8969-0.00430.2004-0.37190.3302-0.0944-0.321-0.37650.11580.07420.12560.06660.04920.00840.110.00710.00290.11340.04010.171729.165825.847919.0485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3980:4056)
2X-RAY DIFFRACTION2(chain A and resid 4057:4103)
3X-RAY DIFFRACTION3(chain A and resid 4104:4315)
4X-RAY DIFFRACTION4(chain A and resid 4316:4366)

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