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- PDB-8r7o: HUWE1 WWE domain in complex with 2'F-ATP -

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Basic information

Entry
Database: PDB / ID: 8r7o
TitleHUWE1 WWE domain in complex with 2'F-ATP
ComponentsE3 ubiquitin-protein ligase HUWE1
KeywordsLIGASE / WWE domain / nucleotide
Function / homology
Function and homology information


negative regulation of peroxisome proliferator activated receptor signaling pathway / histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / protein branched polyubiquitination / positive regulation of type 2 mitophagy / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / ubiquitin-ubiquitin ligase activity / Golgi organization / protein monoubiquitination ...negative regulation of peroxisome proliferator activated receptor signaling pathway / histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / protein branched polyubiquitination / positive regulation of type 2 mitophagy / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / ubiquitin-ubiquitin ligase activity / Golgi organization / protein monoubiquitination / protein K48-linked ubiquitination / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / membrane fusion / cell differentiation / positive regulation of canonical NF-kappaB signal transduction / Golgi membrane / Neutrophil degranulation / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
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) / WWE domain / UBA-like domain / WWE domain superfamily / WWE domain / WWE domain profile. ...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 / WWE domain superfamily / WWE domain / WWE domain profile. / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / 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
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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
DepositionNov 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)43,22610
Polymers42,0784
Non-polymers1,1486
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.915, 62.915, 231.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1616 through 1632 or resid 1634...
d_2ens_1(chain "B" and (resid 1616 through 1625 or (resid 1626...
d_3ens_1(chain "C" and (resid 1616 through 1625 or (resid 1626...
d_4ens_1(chain "D" and (resid 1616 through 1632 or resid 1634...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNALAALAAA1616 - 16327 - 23
d_12ASNASNASNASNAA1634 - 163525 - 26
d_13THRTHRASPASPAA1637 - 163928 - 30
d_14ALAALALYSLYSAA1641 - 164332 - 34
d_15GLYGLYVALVALAA1645 - 164936 - 40
d_16PHEPHEGLUGLUAA1651 - 167042 - 61
d_17THRTHRASNASNAA1672 - 167463 - 65
d_18ARGARGASNASNAA1676 - 168967 - 80
d_21ASNASNALAALABB1616 - 16327 - 23
d_22ASNASNASNASNBB1634 - 163525 - 26
d_23THRTHRASPASPBB1637 - 163928 - 30
d_24ALAALALYSLYSBB1641 - 164332 - 34
d_25GLYGLYVALVALBB1645 - 164936 - 40
d_26PHEPHEGLUGLUBB1651 - 167042 - 61
d_27THRTHRASNASNBB1672 - 167463 - 65
d_28ARGARGASNASNBB1676 - 168967 - 80
d_31ASNASNALAALACC1616 - 16327 - 23
d_32ASNASNASNASNCC1634 - 163525 - 26
d_33THRTHRASPASPCC1637 - 163928 - 30
d_34ALAALALYSLYSCC1641 - 164332 - 34
d_35GLYGLYVALVALCC1645 - 164936 - 40
d_36PHEPHEGLUGLUCC1651 - 167042 - 61
d_37THRTHRASNASNCC1672 - 167463 - 65
d_38ARGARGASNASNCC1676 - 168967 - 80
d_41ASNASNALAALADD1616 - 16327 - 23
d_42ASNASNASNASNDD1634 - 163525 - 26
d_43THRTHRASPASPDD1637 - 163928 - 30
d_44ALAALALYSLYSDD1641 - 164332 - 34
d_45GLYGLYVALVALDD1645 - 164936 - 40
d_46PHEPHEGLUGLUDD1651 - 167042 - 61
d_47THRTHRASNASNDD1672 - 167463 - 65
d_48ARGARGASNASNDD1676 - 168967 - 80

NCS oper:
IDCodeMatrixVector
1given(0.668638166158, -0.265787737071, 0.694463736691), (-0.241677211538, -0.960909659002, -0.135073138185), (0.703217696151, -0.077521003985, -0.706735711395)3.80140985278, -0.24572241633, -9.12002983534
2given(-0.983171571781, 0.177339342164, -0.0438681907775), (0.151578258187, 0.925928578474, 0.345948405417), (0.101969074166, 0.333477173561, -0.937227444448)-52.2194811137, 9.89625498322, -29.9570061023
3given(-0.728896256814, 0.0779913097084, -0.680167334127), (0.0979987974288, -0.971373442188, -0.216402106078), (-0.677573968291, -0.224390265881, 0.700387411418)-55.6938166106, 7.29375285474, -21.1366239459

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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.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-YGC / [[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 509.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15FN5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
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: X10SA / Wavelength: 0.999824 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999824 Å / Relative weight: 1
ReflectionResolution: 1.36→60.721 Å / Num. obs: 86990 / % possible obs: 86.2 % / Redundancy: 20 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.2
Reflection shellResolution: 1.361→1.45 Å / Num. unique obs: 4348 / CC1/2: 0.649 / % possible all: 25.4

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDS(VERSION Feb 5data reduction
autoPROC(Version 1.1.7)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→42.64 Å / SU ML: 0.1099 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6144
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 4317 4.96 %RANDOM
Rwork0.168 82664 --
obs0.1693 86981 86.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.39 Å2
Refinement stepCycle: LAST / Resolution: 1.36→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 66 376 2894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01162634
X-RAY DIFFRACTIONf_angle_d1.22923597
X-RAY DIFFRACTIONf_chiral_restr0.1015375
X-RAY DIFFRACTIONf_plane_restr0.0133460
X-RAY DIFFRACTIONf_dihedral_angle_d12.0424989
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.32550195439
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.877752573329
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.888100183726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.427910.230640X-RAY DIFFRACTION
1.38-1.390.328490.2418262X-RAY DIFFRACTION
1.39-1.410.3124330.249685X-RAY DIFFRACTION21.87
1.41-1.430.2824630.23331159X-RAY DIFFRACTION37
1.43-1.450.2633870.23591609X-RAY DIFFRACTION51.63
1.45-1.470.27821160.22142357X-RAY DIFFRACTION74.04
1.47-1.490.24581360.20552784X-RAY DIFFRACTION88.32
1.49-1.511433058X-RAY DIFFRACTION97.06
1.51-1.530.24891660.18623188X-RAY DIFFRACTION99.55
1.53-1.560.23611730.17743101X-RAY DIFFRACTION100
1.56-1.590.22121670.17453155X-RAY DIFFRACTION100
1.59-1.610.21221700.16483182X-RAY DIFFRACTION100
1.61-1.640.19271570.16633151X-RAY DIFFRACTION100
1.64-1.680.20991640.16323168X-RAY DIFFRACTION100
1.68-1.720.18291940.16123153X-RAY DIFFRACTION100
1.72-1.750.19321780.163143X-RAY DIFFRACTION100
1.75-1.80.19181870.17133158X-RAY DIFFRACTION100
1.8-1.850.22171560.17043192X-RAY DIFFRACTION100
1.85-1.90.21131580.1533187X-RAY DIFFRACTION100
1.9-1.960.1731840.14813162X-RAY DIFFRACTION100
1.96-2.030.18861500.14913214X-RAY DIFFRACTION100
2.03-2.110.18491680.15463185X-RAY DIFFRACTION100
2.11-2.210.17731830.1563189X-RAY DIFFRACTION100
2.21-2.330.21491670.16553240X-RAY DIFFRACTION100
2.33-2.470.26031580.17673238X-RAY DIFFRACTION100
2.47-2.660.20421740.17923221X-RAY DIFFRACTION100
2.66-2.930.21111730.17623268X-RAY DIFFRACTION100
2.93-3.361403324X-RAY DIFFRACTION100
3.36-4.230.17421810.14833340X-RAY DIFFRACTION99.97

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