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- PDB-4cfg: Structure of the TRIM25 coiled-coil -

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Basic information

Entry
Database: PDB / ID: 4cfg
TitleStructure of the TRIM25 coiled-coil
ComponentsE3 UBIQUITIN/ISG15 LIGASE TRIM25
KeywordsLIGASE
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 / ERAD pathway / 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 / 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 / ERAD pathway / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / protein monoubiquitination / antiviral innate immune response / TRAF6 mediated NF-kB activation / ligase activity / viral release from host cell / protein K48-linked ubiquitination / 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 / ISG15 antiviral mechanism / cytoplasmic stress granule / response to estrogen / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / ubiquitin protein ligase activity / positive regulation of DNA-binding transcription factor activity / Interferon gamma signaling / 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 / cytosol / cytoplasm
Similarity search - Function
TRIM25, PRY/SPRY domain / zinc finger of C3HC4-type, RING / 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 of C3HC4-type, RING / 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
Similarity search - Domain/homology
E3 ubiquitin/ISG15 ligase TRIM25
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsJames, L.
CitationJournal: To be Published
Title: Structure of the Trim25 Coiled-Coil
Authors: James, L.
History
DepositionNov 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)142,8972
Polymers142,8972
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-87.5 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.880, 68.780, 100.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 71448.484 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q14258, ubiquitin-protein ligase, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 50 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Type: DIAMOND / Wavelength: 1.5
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.8→57 Å / Num. obs: 8805 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7

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Processing

SoftwareName: REFMAC / Version: 5.7.0002 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.8→56.88 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / SU B: 48.703 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.5
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30914 975 10 %RANDOM
Rwork0.25106 ---
obs0.25685 8805 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.511 Å2
Baniso -1Baniso -2Baniso -3
1-5.21 Å20 Å20 Å2
2--2.75 Å20 Å2
3----7.96 Å2
Refinement stepCycle: LAST / Resolution: 2.8→56.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 0 8 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192683
X-RAY DIFFRACTIONr_bond_other_d0.0040.021913
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9873591
X-RAY DIFFRACTIONr_angle_other_deg1.37734694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2325.259135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.80515562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5541522
X-RAY DIFFRACTIONr_chiral_restr0.0950.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022896
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02482
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 61 -
Rwork0.397 555 -
obs--89.53 %
Refinement TLS params.

Method: refined / 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)
10.86210.24983.09850.31141.299115.5037-0.11750.0475-0.0157-0.0431-0.03760.0866-0.83890.6840.15510.0697-0.0870.03060.1948-0.04980.195136.509914.212760.4344
20.98820.00463.37970.17-0.096516.7553-0.07610.0341-0.0143-0.0031-0.06680.0732-0.7642-0.03150.14290.05760.0168-0.00380.0356-0.0440.228526.869512.908638.9191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A194 - 357
2X-RAY DIFFRACTION2B195 - 356

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