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- PDB-8rd0: HUWE1 WWE domain in complex with compound 3 -

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Basic information

Entry
Database: PDB / ID: 8rd0
TitleHUWE1 WWE domain in complex with compound 3
ComponentsE3 ubiquitin-protein ligase HUWE1
KeywordsLIGASE / WWE domain
Function / homology
Function and homology information


negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / protein monoubiquitination / Golgi organization / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair ...negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / protein monoubiquitination / Golgi organization / 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 / cytoplasm / cytosol
Similarity search - Function
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) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain / WWE domain superfamily / WWE 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) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain / 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 / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Armadillo-type fold
Similarity search - Domain/homology
Chem-51X / E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.765 Å
AuthorsMuenzker, L. / Boettcher, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)875510European Union
CitationJournal: Commun Biol / Year: 2024
Title: A ligand discovery toolbox for the WWE domain family of human E3 ligases
Authors: Munzker, L. / Kimani, S.W. / Fowkes, M.M. / Dong, A. / Zheng, H. / Li, Y. / Dasovich, M. / Zak, K.M. / Leung, A.K.L. / Elkins, J.M. / Kessler, D. / Arrowsmith, C.H. / Halabelian, L. / Bottcher, J.
History
DepositionDec 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,70112
Polymers42,0784
Non-polymers6238
Water6,846380
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-111 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.795, 62.795, 231.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-1977-

HOH

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Components

#1: Protein
E3 ubiquitin-protein ligase HUWE1


Mass: 10519.563 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUWE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6Z7
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-51X / (1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)acetic acid


Mass: 205.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 278 K / Method: vapor diffusion / Details: 0.1 M Na Acetate pH 4.83, 2.9 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.765→60.61 Å / Num. obs: 42066 / % possible obs: 95.1 % / Redundancy: 23 % / CC1/2: 0.998 / Net I/σ(I): 13.4
Reflection shellResolution: 1.765→1.86 Å / Num. unique obs: 2102 / CC1/2: 0.601

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Processing

Software
NameVersionClassification
XDS(VERSION Jan 31data reduction
autoPROC(Version 1.1.7)data scaling
STARANISOdata scaling
BUSTER2.11.8 (26-JUL-2023)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.765→25.27 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.123 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.103
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT ELECTRON-CLOUD POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 2067 4.92 %RANDOM
Rwork0.1967 ---
obs0.1975 42039 89.8 %-
Displacement parametersBiso mean: 33.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.0063 Å20 Å20 Å2
2---0.0063 Å20 Å2
3---0.0126 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.765→25.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 36 380 2892
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095002HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.888886HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1548SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes832HARMONIC5
X-RAY DIFFRACTIONt_it5002HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion13.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion322SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5104SEMIHARMONIC4
LS refinement shellResolution: 1.765→1.83 Å
RfactorNum. reflection% reflection
Rfree0.2715 -4.52 %
Rwork0.2549 803 -
obs--18.18 %
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)
12.7507-0.3401-0.2460.209-0.0980.06210.07290.38750.0855-0.0866-0.06250.0239-0.06810.0258-0.0103-0.01640.0158-0.01710.09260.0012-0.041-9.63091.9104-19.5192
20.27890.13671.21040.26450.05141.6362-0.0041-0.127-0.00280.0853-0.02470.0974-0.0651-0.2960.0288-0.0410.02110.0270.0807-0.03030.0268-16.99252.8315-2.2285
33.04881.4705-1.5181.3789-0.579900.1857-0.33220.02350.1519-0.2392-0.0318-0.00940.08510.0534-0.044-0.0218-0.00290.08190.0461-0.0274-41.34193.5196-11.8128
40-0.32431.00752.5373-1.50721.62160.01410.1680.1297-0.1943-0.085-0.22250.13270.10790.071-0.06250.00340.04530.06630.0678-0.0093-34.84298.2311-28.659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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