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- PDB-4b8e: PRY-SPRY domain of Trim25 -

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Basic information

Entry
Database: PDB / ID: 4b8e
TitlePRY-SPRY domain of Trim25
ComponentsE3 UBIQUITIN/ISG15 LIGASE TRIM25
KeywordsLIGASE
Function / homology
Function and homology information


: / suppression of viral release by host => GO:0044790 / : / RIG-I binding / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / : / regulation of viral entry into host cell / negative regulation of viral entry into host cell / response to vitamin D ...: / suppression of viral release by host => GO:0044790 / : / RIG-I binding / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / : / regulation of viral entry into host cell / negative regulation of viral entry into host cell / response to vitamin D / protein monoubiquitination / ligase activity / cellular response to leukemia inhibitory factor / RING-type E3 ubiquitin transferase / positive regulation of DNA-binding transcription factor activity / cytoplasmic stress granule / response to estrogen / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / nuclear body / innate immune response / nucleoplasm / metal ion binding / cytoplasm / cytosol
Similarity search - Function
TRIM25, PRY/SPRY domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain ...TRIM25, PRY/SPRY domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin/ISG15 ligase TRIM25
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.779 Å
AuthorsKershaw, N.J. / D'Cruz, A.A. / Nicola, N.A. / Nicholson, S.E. / Babon, J.J.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal Structure of the Trim25 B30.2 (Pryspry) Domain: A Key Component of Antiviral Signaling.
Authors: D'Cruz, A.A. / Kershaw, N.J. / Chiang, J.J. / Wang, M.K. / Nicola, N.A. / Babon, J.J. / Gack, M.U. / Nicholson, S.E.
History
DepositionAug 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1649
Polymers44,8892
Non-polymers2757
Water4,035224
1
A: E3 UBIQUITIN/ISG15 LIGASE TRIM25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6847
Polymers22,4451
Non-polymers2396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 UBIQUITIN/ISG15 LIGASE TRIM25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4802
Polymers22,4451
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.149, 73.561, 91.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-2134-

HOH

21B-2005-

HOH

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Components

#1: Protein E3 UBIQUITIN/ISG15 LIGASE TRIM25 / ESTROGEN-RESPONSIVE FINGER PROTEIN / TRIPARTITE MOTIF-CONTAINING PROTEIN 25 / UBIQUITIN/ISG15- ...ESTROGEN-RESPONSIVE FINGER PROTEIN / TRIPARTITE MOTIF-CONTAINING PROTEIN 25 / UBIQUITIN/ISG15-CONJUGATING ENZYME TRIM25 / ZINC FINGER PROTEIN 147


Mass: 22444.633 Da / Num. of mol.: 2 / Fragment: PRYSPRY / B30.2, RESIDUES 440-634
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q61510, ubiquitin-protein ligase, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.13 Å3/Da / Density % sol: 34.6 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 0.2M NACL, 0.1M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.78→91.01 Å / Num. obs: 38142 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 25.68 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.9
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WL1

2wl1


Resolution: 1.779→45.505 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 1902 5 %
Rwork0.1734 --
obs0.1744 38055 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 32.4 Å2
Refinement stepCycle: LAST / Resolution: 1.779→45.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 10 224 3248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073114
X-RAY DIFFRACTIONf_angle_d0.9984245
X-RAY DIFFRACTIONf_dihedral_angle_d12.0231048
X-RAY DIFFRACTIONf_chiral_restr0.077470
X-RAY DIFFRACTIONf_plane_restr0.004535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7791-1.82350.24211320.23112503X-RAY DIFFRACTION98
1.8235-1.87290.27921360.21722557X-RAY DIFFRACTION100
1.8729-1.9280.26241320.20032539X-RAY DIFFRACTION100
1.928-1.99020.22491350.18692551X-RAY DIFFRACTION100
1.9902-2.06130.19261340.17882540X-RAY DIFFRACTION100
2.0613-2.14390.20921340.17292564X-RAY DIFFRACTION100
2.1439-2.24140.20311350.16692575X-RAY DIFFRACTION100
2.2414-2.35960.22751350.18082563X-RAY DIFFRACTION100
2.3596-2.50740.211380.18192594X-RAY DIFFRACTION100
2.5074-2.7010.25441360.18772586X-RAY DIFFRACTION100
2.701-2.97280.17011360.18592580X-RAY DIFFRACTION100
2.9728-3.40280.20921360.17442608X-RAY DIFFRACTION100
3.4028-4.28670.15341400.15682653X-RAY DIFFRACTION100
4.2867-45.51940.17521430.15962740X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -15.3459 Å / Origin y: -5.228 Å / Origin z: -13.0637 Å
111213212223313233
T0.1417 Å2-0.0098 Å20.0539 Å2-0.21 Å2-0.0478 Å2--0.1822 Å2
L0.9091 °2-0.4494 °20.6028 °2-1.9421 °2-0.7149 °2--1.8506 °2
S0.0591 Å °0.1622 Å °-0.0619 Å °-0.184 Å °-0.021 Å °-0.2608 Å °0.1276 Å °0.3815 Å °-0.0437 Å °
Refinement TLS groupSelection details: ALL

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