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- PDB-8pd6: Crystal structure of the TRIM58 PRY-SPRY domain in complex with T... -

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Basic information

Entry
Database: PDB / ID: 8pd6
TitleCrystal structure of the TRIM58 PRY-SPRY domain in complex with TRIM-473
ComponentsE3 ubiquitin-protein ligase TRIM58
KeywordsTRANSFERASE / E3 ligase / TRIM58 / PRY-SPRY
Function / homology
Function and homology information


positive regulation of erythrocyte enucleation / regulation of nuclear migration along microtubule / regulation of viral entry into host cell / dynein heavy chain binding / dynein intermediate chain binding / protein autoubiquitination / positive regulation of autophagy / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin protein ligase activity ...positive regulation of erythrocyte enucleation / regulation of nuclear migration along microtubule / regulation of viral entry into host cell / dynein heavy chain binding / dynein intermediate chain binding / protein autoubiquitination / positive regulation of autophagy / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin protein ligase activity / regulation of protein localization / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / innate immune response / protein kinase binding / protein homodimerization activity / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase TRIM58, PRY/SPRY domain / E3 ubiquitin-protein ligase TRIM58, RING finger, HC subclass / zinc finger of C3HC4-type, RING / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger ...E3 ubiquitin-protein ligase TRIM58, PRY/SPRY domain / E3 ubiquitin-protein ligase TRIM58, RING finger, HC subclass / zinc finger of C3HC4-type, RING / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-YCB / E3 ubiquitin-protein ligase TRIM58
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsRenatus, M. / Hoegenauer, K. / Schroeder, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Discovery of Ligands for TRIM58, a Novel Tissue-Selective E3 Ligase.
Authors: Hoegenauer, K. / An, S. / Axford, J. / Benander, C. / Bergsdorf, C. / Botsch, J. / Chau, S. / Fernandez, C. / Gleim, S. / Hassiepen, U. / Hunziker, J. / Joly, E. / Keller, A. / Lopez Romero, ...Authors: Hoegenauer, K. / An, S. / Axford, J. / Benander, C. / Bergsdorf, C. / Botsch, J. / Chau, S. / Fernandez, C. / Gleim, S. / Hassiepen, U. / Hunziker, J. / Joly, E. / Keller, A. / Lopez Romero, S. / Maher, R. / Mangold, A.S. / Mickanin, C. / Mihalic, M. / Neuner, P. / Patterson, A.W. / Perruccio, F. / Roggo, S. / Scesa, J. / Schroder, M. / Shkoza, D. / Thai, B. / Vulpetti, A. / Renatus, M. / Reece-Hoyes, J.S.
History
DepositionJun 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7996
Polymers24,2351
Non-polymers5655
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-13 kcal/mol
Surface area8670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.284, 55.284, 202.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

21A-722-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein E3 ubiquitin-protein ligase TRIM58 / Protein BIA2 / RING-type E3 ubiquitin transferase TRIM58 / Tripartite motif-containing protein 58


Mass: 24234.566 Da / Num. of mol.: 1 / Mutation: C266S C278S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM58 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NG06, RING-type E3 ubiquitin transferase

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Non-polymers , 5 types, 156 molecules

#2: Chemical ChemComp-YCB / ~{N}2-[3-(dimethylamino)propyl]-6-phenyl-~{N}4-(piperidin-4-ylmethyl)quinazoline-2,4-diamine


Mass: 418.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H34N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.85 Å3/Da / Density % sol: 33.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% (w/v) PEG 3550, 0.2 M MgCl2, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→20.01 Å / Num. obs: 46465 / % possible obs: 100 % / Redundancy: 18.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.026 / Rrim(I) all: 0.115 / Χ2: 0.66 / Net I/σ(I): 12
Reflection shellResolution: 1.3→1.32 Å / % possible obs: 100 % / Redundancy: 18.6 % / Rmerge(I) obs: 0.959 / Num. measured all: 42380 / Num. unique obs: 2274 / CC1/2: 0.806 / Rpim(I) all: 0.228 / Rrim(I) all: 0.986 / Χ2: 0.22 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→20.01 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.649 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 2323 5 %RANDOM
Rwork0.13866 ---
obs0.14054 44022 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.655 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.07 Å2-0 Å2
2---0.15 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.3→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 38 151 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131601
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151446
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.672201
X-RAY DIFFRACTIONr_angle_other_deg1.4921.5693351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2535201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02321.92378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48915242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1871510
X-RAY DIFFRACTIONr_chiral_restr0.3770.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021839
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02365
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6341.506777
X-RAY DIFFRACTIONr_mcbond_other2.5121.503776
X-RAY DIFFRACTIONr_mcangle_it2.8552.26987
X-RAY DIFFRACTIONr_mcangle_other2.8822.263988
X-RAY DIFFRACTIONr_scbond_it3.1431.769824
X-RAY DIFFRACTIONr_scbond_other3.1421.771825
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9962.571215
X-RAY DIFFRACTIONr_long_range_B_refined3.89518.5831775
X-RAY DIFFRACTIONr_long_range_B_other3.73218.2521750
X-RAY DIFFRACTIONr_rigid_bond_restr3.72133046
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 186 -
Rwork0.207 3176 -
obs--100 %

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