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- PDB-6fln: Crystal structure of the human TRIM25 coiled-coil and PRYSPRY domains -

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Basic information

Entry
Database: PDB / ID: 6fln
TitleCrystal structure of the human TRIM25 coiled-coil and PRYSPRY domains
ComponentsE3 ubiquitin/ISG15 ligase TRIM25
KeywordsPROTEIN BINDING / Coiled-coil / PRYSPRY domain / TRIM proteins / 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 / 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 / ligase activity / TRAF6 mediated NF-kB activation / 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 / DDX58/IFIH1-mediated induction of interferon-alpha/beta / RING-type E3 ubiquitin transferase / PKR-mediated signaling / ISG15 antiviral mechanism / cytoplasmic stress granule / positive regulation of DNA-binding transcription factor activity / response to estrogen / ubiquitin-protein transferase activity / regulation of protein localization / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase 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, 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. ...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. / 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 / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsCusack, S. / Lethier, M.
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 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
E: E3 ubiquitin/ISG15 ligase TRIM25


Theoretical massNumber of molelcules
Total (without water)150,8653
Polymers150,8653
Non-polymers00
Water0
1
A: E3 ubiquitin/ISG15 ligase TRIM25
B: E3 ubiquitin/ISG15 ligase TRIM25


Theoretical massNumber of molelcules
Total (without water)100,5772
Polymers100,5772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-99 kcal/mol
Surface area38650 Å2
MethodPISA
2
E: E3 ubiquitin/ISG15 ligase TRIM25

E: E3 ubiquitin/ISG15 ligase TRIM25


Theoretical massNumber of molelcules
Total (without water)100,5772
Polymers100,5772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area12770 Å2
ΔGint-99 kcal/mol
Surface area38360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.920, 89.920, 827.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13B
23E

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA189 - 6284 - 443
21SERSERBB189 - 6284 - 443
12PROPROAA189 - 6294 - 444
22PROPROEC189 - 6294 - 444
13PROPROBB189 - 6294 - 444
23PROPROEC189 - 6294 - 444

NCS ensembles :
ID
1
2
3

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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: 50288.484 Da / Num. of mol.: 3 / Fragment: coiled-coil and PRYSPRY domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM25, EFP, RNF147, ZNF147 / 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

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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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 10 mg/ml was mixed in 2:1 ratio with mother liquor containing 0.2 M sodium formate, 14% PEG 3350 and 0.1 M bis-Tris pH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 3.6→137.85 Å / Num. obs: 24552 / % possible obs: 99.5 % / Redundancy: 5.36 % / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.151 / Net I/σ(I): 8.18
Reflection shellResolution: 3.6→3.69 Å / Redundancy: 5.51 % / Rmerge(I) obs: 2.38 / CC1/2: 0.569 / Rrim(I) all: 2.64 / Χ2: 0.75 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Separate coiled-coil (PDB:4LTB) and PRYSPRY (PDB:6FLM) domains

4ltb

6flm


Resolution: 3.6→137.85 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 75.375 / SU ML: 0.929 / Cross valid method: THROUGHOUT / ESU R Free: 0.722 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31844 1255 5.1 %RANDOM
Rwork0.28717 ---
obs0.28877 23260 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 219.61 Å2
Baniso -1Baniso -2Baniso -3
1-8.14 Å24.07 Å20 Å2
2--8.14 Å20 Å2
3----26.42 Å2
Refinement stepCycle: 1 / Resolution: 3.6→137.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8861 0 0 0 8861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199035
X-RAY DIFFRACTIONr_bond_other_d0.0010.028477
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.95412188
X-RAY DIFFRACTIONr_angle_other_deg0.854319709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09251091
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09324.129419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.898151695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3421557
X-RAY DIFFRACTIONr_chiral_restr0.060.21361
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029859
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021826
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_it9.11222.2234382
X-RAY DIFFRACTIONr_mcbond_other9.11122.2224381
X-RAY DIFFRACTIONr_mcangle_it15.17933.3285467
X-RAY DIFFRACTIONr_mcangle_other15.17833.3285468
X-RAY DIFFRACTIONr_scbond_it7.01622.7444651
X-RAY DIFFRACTIONr_scbond_other7.01522.7454652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.46733.936721
X-RAY DIFFRACTIONr_long_range_B_refined20.94310258
X-RAY DIFFRACTIONr_long_range_B_other20.94210259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A222160.06
12B222160.06
21A222140.05
22E222140.05
31B223220.05
32E223220.05
LS refinement shellResolution: 3.602→3.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.538 69 -
Rwork0.583 1598 -
obs--97.31 %

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