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- PDB-9i0t: Crystal structure of TRIM25 PRYSPRY covalently bound to 2-chloro-... -

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Basic information

Entry
Database: PDB / ID: 9i0t
TitleCrystal structure of TRIM25 PRYSPRY covalently bound to 2-chloro-1-[4-(3-methyl-4-phenyl-phenyl)carbonyl-1,4-diazepan-1-yl]ethanone
ComponentsE3 ubiquitin/ISG15 ligase TRIM25
KeywordsLIGASE / Ubiquitin / E3 Ligase / small molecule ligand / PRYSPRY
Function / homology
Function and homology information


: / RIG-I binding / regulation of viral entry into host cell / suppression of viral release by host / host-mediated suppression of symbiont invasion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Modulation of host responses by IFN-stimulated genes / response to vitamin D / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway ...: / RIG-I binding / regulation of viral entry into host cell / suppression of viral release by host / host-mediated suppression of symbiont invasion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / Modulation of host responses by IFN-stimulated genes / response to vitamin D / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / ligase activity / RSV-host interactions / TRAF6 mediated NF-kB activation / viral release from host cell / protein monoubiquitination / positive regulation of DNA-binding transcription factor activity / protein K48-linked ubiquitination / ERAD pathway / antiviral innate immune response / Negative regulators of DDX58/IFIH1 signaling / cellular response to leukemia inhibitory factor / Termination of translesion DNA synthesis / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / positive regulation of NF-kappaB transcription factor activity / PKR-mediated signaling / RING-type E3 ubiquitin transferase / SARS-CoV-1 activates/modulates innate immune responses / response to estrogen / Ovarian tumor domain proteases / cytoplasmic stress granule / Interferon gamma signaling / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of protein localization / TRAF3-dependent IRF activation pathway / response to oxidative stress / ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / nuclear body / cadherin binding / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
TRIM25, PRY/SPRY domain / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain ...TRIM25, PRY/SPRY domain / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / 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/ISG15 ligase TRIM25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMcPhie, K.A. / Esposito, D. / Rittinger, K.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2075 United Kingdom
Wellcome TrustCC2075 United Kingdom
Cancer Research UKCC2075 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2075 United Kingdom
CitationJournal: Chem Sci / Year: 2025
Title: Discovery and optimisation of a covalent ligand for TRIM25 and its application to targeted protein ubiquitination.
Authors: McPhie, K.A. / Esposito, D. / Pettinger, J. / Norman, D. / Werner, T. / Mathieson, T. / Bush, J.T. / Rittinger, K.
History
DepositionJan 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin/ISG15 ligase TRIM25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0322
Polymers22,6951
Non-polymers3361
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9720 Å2
Unit cell
Length a, b, c (Å)44.360, 68.782, 69.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein E3 ubiquitin/ISG15 ligase TRIM25 / Estrogen-responsive finger protein / RING finger protein 147 / RING-type E3 ubiquitin transferase / ...Estrogen-responsive finger protein / RING finger protein 147 / RING-type E3 ubiquitin transferase / RING-type E3 ubiquitin transferase TRIM25 / Tripartite motif-containing protein 25 / Ubiquitin/ISG15-conjugating enzyme TRIM25 / Zinc finger protein 147


Mass: 22695.189 Da / Num. of mol.: 1 / Fragment: PRYSPRY domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM25, EFP, RNF147, ZNF147 / Production host: Escherichia coli (E. coli)
References: UniProt: Q14258, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases), RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-A1IZK / 1-[4-(3-methyl-4-phenyl-phenyl)carbonyl-1,4-diazepan-1-yl]ethanone


Mass: 336.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES, 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→49 Å / Num. obs: 20050 / % possible obs: 97.64 % / Redundancy: 12 % / Biso Wilson estimate: 20.21 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05966 / Rpim(I) all: 0.01753 / Rrim(I) all: 0.06225 / Net I/σ(I): 20.98
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.3006 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 2585 / CC1/2: 0.974 / CC star: 0.993 / Rpim(I) all: 0.1093 / Rrim(I) all: 0.3213 / % possible all: 89.86

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49 Å / SU ML: 0.2187 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2449 971 4.87 %
Rwork0.2215 18951 -
obs0.2227 19922 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1583 0 25 84 1692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581656
X-RAY DIFFRACTIONf_angle_d0.80262248
X-RAY DIFFRACTIONf_chiral_restr0.057238
X-RAY DIFFRACTIONf_plane_restr0.0058281
X-RAY DIFFRACTIONf_dihedral_angle_d12.9662597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.90.30561290.23272440X-RAY DIFFRACTION89.86
1.9-2.010.35421230.29952624X-RAY DIFFRACTION96.02
2.01-2.170.29451460.23542722X-RAY DIFFRACTION99.83
2.17-2.390.30461550.26472671X-RAY DIFFRACTION97.72
2.39-2.730.23771330.23832763X-RAY DIFFRACTION99.97
2.73-3.440.24661350.22212810X-RAY DIFFRACTION99.97
3.44-490.18951500.18212921X-RAY DIFFRACTION99.87

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