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- PDB-6flm: Crystal structure of the human TRIM25 PRYSPRY domain -

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Basic information

Entry
Database: PDB / ID: 6flm
TitleCrystal structure of the human TRIM25 PRYSPRY domain
ComponentsE3 ubiquitin/ISG15 ligase TRIM25
KeywordsPROTEIN BINDING / PRYSPRY domain / TRIM protein / E3 ligase
Function / homology
Function and homology information


: / RIG-I binding / regulation of viral entry into host cell / suppression of viral release by host / negative regulation of viral entry into host cell / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / response to vitamin D / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / RSV-host interactions ...: / RIG-I binding / regulation of viral entry into host cell / suppression of viral release by host / negative regulation of viral entry into host cell / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / response to vitamin D / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / RSV-host interactions / protein monoubiquitination / ligase activity / TRAF6 mediated NF-kB activation / antiviral innate immune response / viral release from host cell / protein K48-linked ubiquitination / ERAD pathway / cellular response to leukemia inhibitory factor / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / RING-type E3 ubiquitin transferase / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / positive regulation of DNA-binding transcription factor activity / cytoplasmic stress granule / response to estrogen / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / Interferon gamma signaling / ubiquitin protein ligase activity / Ovarian tumor domain proteases / positive regulation of NF-kappaB transcription factor activity / TRAF3-dependent IRF activation pathway / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / response to oxidative stress / transcription coactivator activity / nuclear body / cadherin binding / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / nucleoplasm / metal ion binding / cytoplasm / cytosol
Similarity search - Function
TRIM25, PRY/SPRY domain / 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 / 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. / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.009 Å
AuthorsCusack, S. / Kowalinski, E.
Funding support France, 1items
OrganizationGrant numberCountry
ERC322586 France
CitationJournal: Nat Commun / Year: 2018
Title: Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition.
Authors: Koliopoulos, M.G. / Lethier, M. / van der Veen, A.G. / Haubrich, K. / Hennig, J. / Kowalinski, E. / Stevens, R.V. / Martin, S.R. / Reis E Sousa, C. / Cusack, S. / Rittinger, K.
History
DepositionJan 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,37017
Polymers68,0863
Non-polymers1,28414
Water9,206511
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A: E3 ubiquitin/ISG15 ligase TRIM25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2727
Polymers22,6951
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin/ISG15 ligase TRIM25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8873
Polymers22,6951
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin/ISG15 ligase TRIM25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2117
Polymers22,6951
Non-polymers5166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.750, 152.750, 68.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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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.: 3 / Fragment: PRYSPRY domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM25, EFP, RNF147, ZNF147 / Plasmid: pFastBacHtb / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q14258, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases), RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 3.41 Å3/Da / Density % sol: 63.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15 mg/ml protein mixed in 1:1 ratio with reservoir containing 0.1 M bis-TRIS pH 6.5 and 2M ammonium sulphate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.009→47.735 Å / Num. obs: 52640 / % possible obs: 84.1 % / Redundancy: 5.34 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.135 / Net I/σ(I): 11.42
Reflection shellResolution: 2.01→2.1 Å / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.36 / CC1/2: 0.837 / Rrim(I) all: 0.412

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.009→47.735 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 2659 5.05 %RANDOM
Rwork0.1649 ---
obs0.167 52636 85.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.009→47.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4766 0 66 511 5343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055046
X-RAY DIFFRACTIONf_angle_d0.7076872
X-RAY DIFFRACTIONf_dihedral_angle_d13.3052935
X-RAY DIFFRACTIONf_chiral_restr0.053733
X-RAY DIFFRACTIONf_plane_restr0.004855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0093-2.04580.2828970.2481559X-RAY DIFFRACTION51
2.0458-2.08520.2714910.20711895X-RAY DIFFRACTION62
2.0852-2.12770.2451070.20791852X-RAY DIFFRACTION61
2.1277-2.1740.2266920.19261913X-RAY DIFFRACTION62
2.174-2.22460.26821110.18851890X-RAY DIFFRACTION62
2.2246-2.28020.22151000.18151894X-RAY DIFFRACTION62
2.2802-2.34190.22041020.17341908X-RAY DIFFRACTION63
2.3419-2.41080.24121490.18352896X-RAY DIFFRACTION95
2.4108-2.48860.211750.18383057X-RAY DIFFRACTION100
2.4886-2.57750.22751590.17783101X-RAY DIFFRACTION100
2.5775-2.68070.20571440.17123077X-RAY DIFFRACTION100
2.6807-2.80270.22911530.1683078X-RAY DIFFRACTION100
2.8027-2.95040.21691620.16383112X-RAY DIFFRACTION100
2.9504-3.13530.19711700.16493083X-RAY DIFFRACTION100
3.1353-3.37730.2191730.15913071X-RAY DIFFRACTION100
3.3773-3.7170.19381780.14723096X-RAY DIFFRACTION100
3.717-4.25460.17281780.13263098X-RAY DIFFRACTION100
4.2546-5.35920.16841540.13193148X-RAY DIFFRACTION100
5.3592-47.74830.20821640.2013249X-RAY DIFFRACTION100

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