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- PDB-9iun: Crystal structure of Trim25 Pspry -

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Basic information

Entry
Database: PDB / ID: 9iun
TitleCrystal structure of Trim25 Pspry
ComponentsE3 ubiquitin/ISG15 ligase TRIM25
KeywordsLIGASE / Trim25
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 / response to estrogen / SARS-CoV-1 activates/modulates innate immune responses / 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: 2.698 Å
AuthorsLi, Y.L. / Lin, T.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of TRIM25 regulation of RIG-I
Authors: Li, Y.L. / Lin, T.W.
History
DepositionJul 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: 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/ISG15 ligase TRIM25
B: E3 ubiquitin/ISG15 ligase TRIM25
C: E3 ubiquitin/ISG15 ligase TRIM25
D: E3 ubiquitin/ISG15 ligase TRIM25
E: E3 ubiquitin/ISG15 ligase TRIM25
F: E3 ubiquitin/ISG15 ligase TRIM25
G: E3 ubiquitin/ISG15 ligase TRIM25
H: E3 ubiquitin/ISG15 ligase TRIM25
I: E3 ubiquitin/ISG15 ligase TRIM25
J: E3 ubiquitin/ISG15 ligase TRIM25
K: E3 ubiquitin/ISG15 ligase TRIM25
L: E3 ubiquitin/ISG15 ligase TRIM25


Theoretical massNumber of molelcules
Total (without water)282,90212
Polymers282,90212
Non-polymers00
Water6,215345
1
A: E3 ubiquitin/ISG15 ligase TRIM25
B: E3 ubiquitin/ISG15 ligase TRIM25
C: E3 ubiquitin/ISG15 ligase TRIM25
D: E3 ubiquitin/ISG15 ligase TRIM25
E: E3 ubiquitin/ISG15 ligase TRIM25
F: E3 ubiquitin/ISG15 ligase TRIM25


Theoretical massNumber of molelcules
Total (without water)141,4516
Polymers141,4516
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: E3 ubiquitin/ISG15 ligase TRIM25
H: E3 ubiquitin/ISG15 ligase TRIM25
I: E3 ubiquitin/ISG15 ligase TRIM25
J: E3 ubiquitin/ISG15 ligase TRIM25
K: E3 ubiquitin/ISG15 ligase TRIM25
L: E3 ubiquitin/ISG15 ligase TRIM25


Theoretical massNumber of molelcules
Total (without water)141,4516
Polymers141,4516
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.015, 182.015, 221.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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: 23575.127 Da / Num. of mol.: 12
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.92 Å3/Da / Density % sol: 68.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM Na citrate pH5.0 and 4 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.698→50 Å / Num. obs: 116665 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 3.9
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.138 / Num. unique obs: 110794

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.698→47.51 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.887 / SU B: 11.176 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / ESU R: 0.441 / ESU R Free: 0.303
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2648 5780 4.958 %
Rwork0.2117 110794 -
all0.214 --
obs-116574 99.92 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.322 Å2
Baniso -1Baniso -2Baniso -3
1--0.717 Å2-0.359 Å2-0 Å2
2---0.717 Å20 Å2
3---2.326 Å2
Refinement stepCycle: LAST / Resolution: 2.698→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18972 0 0 345 19317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01319532
X-RAY DIFFRACTIONr_bond_other_d0.0010.01518047
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.63726513
X-RAY DIFFRACTIONr_angle_other_deg1.2031.57341491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.60352338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60121.866986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.981153185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9721596
X-RAY DIFFRACTIONr_chiral_restr0.0670.22437
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024852
X-RAY DIFFRACTIONr_nbd_refined0.2040.23495
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.217244
X-RAY DIFFRACTIONr_nbtor_refined0.1760.28820
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.29743
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2458
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0790.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1710.259
X-RAY DIFFRACTIONr_nbd_other0.1760.2147
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.213
X-RAY DIFFRACTIONr_mcbond_it3.4693.8569388
X-RAY DIFFRACTIONr_mcbond_other3.4613.8559387
X-RAY DIFFRACTIONr_mcangle_it5.6065.76711714
X-RAY DIFFRACTIONr_mcangle_other5.6065.76811715
X-RAY DIFFRACTIONr_scbond_it3.3824.25210144
X-RAY DIFFRACTIONr_scbond_other3.3824.25210145
X-RAY DIFFRACTIONr_scangle_it5.5716.20414799
X-RAY DIFFRACTIONr_scangle_other5.5716.20514800
X-RAY DIFFRACTIONr_lrange_it8.30442.81520908
X-RAY DIFFRACTIONr_lrange_other8.30542.82720889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.698-2.7680.3874540.3048117X-RAY DIFFRACTION99.9767
2.768-2.8440.3443840.2827952X-RAY DIFFRACTION100
2.844-2.9260.3414000.2557686X-RAY DIFFRACTION100
2.926-3.0160.3083980.257459X-RAY DIFFRACTION100
3.016-3.1150.3023600.2437302X-RAY DIFFRACTION100
3.115-3.2240.3123480.2377023X-RAY DIFFRACTION99.9864
3.224-3.3460.273170.2276829X-RAY DIFFRACTION99.986
3.346-3.4820.2763890.2176491X-RAY DIFFRACTION99.9855
3.482-3.6370.2613140.2126302X-RAY DIFFRACTION99.9849
3.637-3.8150.2483020.1976032X-RAY DIFFRACTION99.9842
3.815-4.0210.223250.1755689X-RAY DIFFRACTION99.9834
4.021-4.2640.2282840.1715414X-RAY DIFFRACTION100
4.264-4.5590.2052500.165141X-RAY DIFFRACTION99.9629
4.559-4.9240.1992620.1634738X-RAY DIFFRACTION99.9201
4.924-5.3930.2462560.1824367X-RAY DIFFRACTION99.9568
5.393-6.0290.2551920.2084007X-RAY DIFFRACTION99.9048
6.029-6.960.3061600.2043567X-RAY DIFFRACTION99.6791
6.96-8.520.241610.1983001X-RAY DIFFRACTION99.9368
8.52-12.0310.2231490.2142347X-RAY DIFFRACTION99.7602
12.031-47.510.363750.3441330X-RAY DIFFRACTION96.3649

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