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- PDB-8pd4: Crystal structure of TRIM58 PRY-SPRY domain -

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Basic information

Entry
Database: PDB / ID: 8pd4
TitleCrystal structure of TRIM58 PRY-SPRY domain
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 / regulation of gene expression / 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
E3 ubiquitin-protein ligase TRIM58
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.714 Å
AuthorsRenatus, M. / 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 / Derived calculations
Category: citation / pdbx_struct_assembly / pdbx_struct_assembly_gen
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
B: E3 ubiquitin-protein ligase TRIM58


Theoretical massNumber of molelcules
Total (without water)48,4692
Polymers48,4692
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.059, 76.531, 107.226
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#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.: 2 / 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 54.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 25% w/v PEG8000, 0.2 M LiCl

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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: Apr 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→62.29 Å / Num. obs: 14294 / % possible obs: 96.5 % / Redundancy: 6.2 % / CC1/2: 0.995 / Net I/σ(I): 7.5
Reflection shellResolution: 2.71→2.72 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 139 / CC1/2: 0.885 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.714→62.29 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 1.271 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.365 / SU Rfree Cruickshank DPI: 0.354
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 710 -RANDOM
Rwork0.2018 ---
obs0.205 14294 96.5 %-
Displacement parametersBiso mean: 34.43 Å2
Baniso -1Baniso -2Baniso -3
1-5.6241 Å20 Å20 Å2
2---9.6031 Å20 Å2
3---3.9789 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.714→62.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 0 268 3412
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083236HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034420HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1060SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes536HARMONIC5
X-RAY DIFFRACTIONt_it3236HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion410SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2530SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion17.87
LS refinement shellResolution: 2.714→2.74 Å
RfactorNum. reflection% reflection
Rfree0.3062 21 -
Rwork0.2471 --
obs--100 %
Refinement TLS params.

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)
10.18630.10840.13630.11420.18911.5539-0.0273-0.01420.0057-0.01420.01580.05220.00570.05220.0116-0.13550.02130.00020.1904-0.0202-0.0841-0.7807-4.800715.353
20.4267-0.08430.45160.00390.00121.1965-0.03110.0445-0.00830.04450.00380.0531-0.00830.05310.0273-0.12710.00450.0020.167-0.0021-0.09510.7822-4.97947.0217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A258 - 461
2X-RAY DIFFRACTION2{ B|* }B258 - 461

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