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- PDB-8rd1: HUWE1 WWE domain in complex with compound 4 -

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Basic information

Entry
Database: PDB / ID: 8rd1
TitleHUWE1 WWE domain in complex with compound 4
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
: / E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å
AuthorsMuenzker, L. / Zak, K.M. / 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

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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)43,00312
Polymers42,0784
Non-polymers9258
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-91 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.768, 62.768, 231.456
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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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.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-YP2 / 2-(2-hydroxy-2-oxoethyl)-1,3-bis(oxidanylidene)isoindole-5-carboxylic acid


Mass: 249.176 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H7NO6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 54.59 %
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: Aug 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.896→60.58 Å / Num. obs: 38225 / % possible obs: 93.2 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Net I/av σ(I): 12.7 / Net I/σ(I): 13.4
Reflection shellResolution: 1.896→1.928 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 532 / CC1/2: 0.647 / % possible all: 30.6

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
STARANISO(Version 1.1.7)data scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.896→25.98 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.159 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1736 -RANDOM
Rwork0.179 ---
obs0.181 35320 93.2 %-
Displacement parametersBiso mean: 32.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.7938 Å20 Å20 Å2
2---0.7938 Å20 Å2
3---1.5876 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.896→25.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 59 378 2921
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085034HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.928933HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1586SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes846HARMONIC5
X-RAY DIFFRACTIONt_it4977HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion322SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4536SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion14.48
LS refinement shellResolution: 1.9→1.93 Å
RfactorNum. reflection% reflection
Rfree0.3184 46 -
Rwork0.2659 --
obs0.2694 707 34.24 %

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