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- PDB-8rd7: HUWE1 WWE domain in complex with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 8rd7
TitleHUWE1 WWE domain in complex with ADP-ribose
ComponentsE3 ubiquitin-protein ligase HUWE1
KeywordsLIGASE / E3 Ligase / Complex / Nucleotide
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
ACETATE ION / Chem-AR6 / E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsMuenzker, L. / Zak, K.M. / Boettcher, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
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)42,96612
Polymers42,0784
Non-polymers8888
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-97 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.883, 62.883, 231.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 439 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / 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: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.31→60.679 Å / Num. obs: 87488 / % possible obs: 78.3 % / Redundancy: 12.9 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 20.5
Reflection shellResolution: 1.313→1.437 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.544 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4372 / Rsym value: 1.544 / % possible all: 16.7

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSJan 31, 202data reduction
autoPROC1.1.7data scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→44.46 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1771 4319 4.94 %RANDOM
Rwork0.1477 ---
obs0.1491 87481 78.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 51 431 2968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d18.3931015
X-RAY DIFFRACTIONf_chiral_restr0.103375
X-RAY DIFFRACTIONf_plane_restr0.013457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.3032400.2364788X-RAY DIFFRACTION22
1.4-1.410.2684450.23451030X-RAY DIFFRACTION30
1.41-1.430.2364650.21451279X-RAY DIFFRACTION36
1.43-1.460.2355830.21591781X-RAY DIFFRACTION51
1.46-1.480.24041560.19442716X-RAY DIFFRACTION78
1.48-1.50.25951640.19073345X-RAY DIFFRACTION96
1.5-1.530.24051760.18283509X-RAY DIFFRACTION100
1.53-1.560.21811720.17133489X-RAY DIFFRACTION100
1.56-1.590.19311680.16313517X-RAY DIFFRACTION100
1.59-1.620.20371930.1523514X-RAY DIFFRACTION100
1.62-1.650.20211750.14653535X-RAY DIFFRACTION100
1.65-1.690.16852080.14363452X-RAY DIFFRACTION100
1.69-1.740.18372020.14573511X-RAY DIFFRACTION100
1.74-1.780.19122060.15673506X-RAY DIFFRACTION100
1.78-1.830.18431650.13343499X-RAY DIFFRACTION100
1.83-1.890.16871810.12563579X-RAY DIFFRACTION100
1.89-1.960.15672040.11733509X-RAY DIFFRACTION100
1.96-2.040.1471830.1163553X-RAY DIFFRACTION100
2.04-2.130.16131760.11463547X-RAY DIFFRACTION100
2.13-2.250.15211910.12213579X-RAY DIFFRACTION100
2.25-2.390.17941890.13093550X-RAY DIFFRACTION100
2.39-2.570.18831780.14663598X-RAY DIFFRACTION100
2.57-2.830.19522050.15953603X-RAY DIFFRACTION100
2.83-3.240.17341530.14733678X-RAY DIFFRACTION100
3.24-4.080.15451990.14193687X-RAY DIFFRACTION100

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