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- PDB-5jw7: Crystal structure of SopA-Trim56 complex -

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Basic information

Entry
Database: PDB / ID: 5jw7
TitleCrystal structure of SopA-Trim56 complex
Components
  • E3 ubiquitin-protein ligase SopA
  • E3 ubiquitin-protein ligase TRIM56
KeywordsLIGASE / Ubiquitination / Bacterial effector / SopA / Trim56
Function / homology
Function and homology information


regulation of type I interferon production / HECT-type E3 ubiquitin transferase / response to type I interferon / protein K63-linked ubiquitination / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / host cell ...regulation of type I interferon production / HECT-type E3 ubiquitin transferase / response to type I interferon / protein K63-linked ubiquitination / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / host cell / defense response to virus / protein ubiquitination / innate immune response / chromatin / positive regulation of DNA-templated transcription / RNA binding / zinc ion binding / extracellular region / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
E3 ubiquitin ligase SopA-like central domain / SopA-like central domain / E3 ubiquitin-protein ligase SopA-like, catalytic domain / SopA-like, catalytic domain superfamily / SopA-like catalytic domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger ...E3 ubiquitin ligase SopA-like central domain / SopA-like central domain / E3 ubiquitin-protein ligase SopA-like, catalytic domain / SopA-like, catalytic domain superfamily / SopA-like catalytic domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase SopA / E3 ubiquitin-protein ligase TRIM56
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.849 Å
AuthorsBhogaraju, S. / Dikic, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for the recognition and degradation of host TRIM proteins by Salmonella effector SopA.
Authors: Fiskin, E. / Bhogaraju, S. / Herhaus, L. / Kalayil, S. / Hahn, M. / Dikic, I.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
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-protein ligase SopA
B: E3 ubiquitin-protein ligase TRIM56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3714
Polymers41,2402
Non-polymers1312
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-14 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.015, 71.015, 122.944
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein E3 ubiquitin-protein ligase SopA / Salmonella outer protein A / Secreted effector protein SopA


Mass: 31218.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: sopA, STM2066 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8ZNR3, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein E3 ubiquitin-protein ligase TRIM56 / RING finger protein 109 / Tripartite motif-containing protein 56


Mass: 10021.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Binds to 2 Zn atoms. / Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM56, RNF109 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BRZ2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 28% w/v Polyacrylate 2100 sodium salt, 0.2M NaCl, 0.1M MES pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.849→43.5 Å / Num. obs: 8375 / % possible obs: 98.37 % / Redundancy: 20 % / Rmerge(I) obs: 0.07443 / Net I/σ(I): 31.15
Reflection shellResolution: 2.849→2.95 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.8347 / Mean I/σ(I) obs: 3.64 / % possible all: 84.05

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QZA, 2CT2

2qza

2ct2


Resolution: 2.849→43.477 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 32.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 791 4.98 %
Rwork0.2234 --
obs0.2261 7542 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.849→43.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 2 1 2387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042446
X-RAY DIFFRACTIONf_angle_d0.9733346
X-RAY DIFFRACTIONf_dihedral_angle_d13.386851
X-RAY DIFFRACTIONf_chiral_restr0.035393
X-RAY DIFFRACTIONf_plane_restr0.005439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8489-3.02730.35811210.28462270X-RAY DIFFRACTION89
3.0273-3.2610.38951370.30032547X-RAY DIFFRACTION100
3.261-3.5890.38261350.26622541X-RAY DIFFRACTION100
3.589-4.1080.31091310.23462584X-RAY DIFFRACTION100
4.108-5.17440.21781310.18532586X-RAY DIFFRACTION100
5.1744-43.48250.24161360.20762574X-RAY DIFFRACTION100

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