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- PDB-4puf: Complex between the Salmonella T3SS effector SlrP and its human t... -

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Basic information

Entry
Database: PDB / ID: 4puf
TitleComplex between the Salmonella T3SS effector SlrP and its human target thioredoxin-1
Components
  • E3 ubiquitin-protein ligase SlrP
  • Thioredoxin
KeywordsLIGASE/OXIDOREDUCTASE / LRR domain / NEL domain / E3 ubiquitin ligase / human thioredoxin 1 / LIGASE -OXIDOREDUCTASE complex / LIGASE-OXIDOREDUCTASE complex
Function / homology
Function and homology information


Protein repair / cellular detoxification of hydrogen peroxide / protein-disulfide reductase [NAD(P)H] activity / positive regulation of peptidyl-cysteine S-nitrosylation / protein secretion by the type III secretion system / Interconversion of nucleotide di- and triphosphates / thioredoxin-disulfide reductase (NADPH) activity / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes ...Protein repair / cellular detoxification of hydrogen peroxide / protein-disulfide reductase [NAD(P)H] activity / positive regulation of peptidyl-cysteine S-nitrosylation / protein secretion by the type III secretion system / Interconversion of nucleotide di- and triphosphates / thioredoxin-disulfide reductase (NADPH) activity / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / positive regulation of DNA binding / response to nitric oxide / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / Purinergic signaling in leishmaniasis infection / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / positive regulation of peptidyl-serine phosphorylation / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Oxidative Stress Induced Senescence / killing of cells of another organism / host cell cytoplasm / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : / Thioredoxin / Leucine-rich repeats, bacterial type / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor ...Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : / Thioredoxin / Leucine-rich repeats, bacterial type / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Thioredoxin domain profile. / Leucine-rich repeat profile. / Thioredoxin domain / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase SlrP / Thioredoxin
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.296 Å
AuthorsZouhir, S. / Bernal-Bayard, J. / Cordero-Alba, M. / Cardenal-Munoz, E. / Guimaraes, B. / Lazar, N. / Ramos-Morales, F. / Nessler, S.
CitationJournal: Biochem.J. / Year: 2014
Title: The structure of the Slrp-Trx1 complex sheds light on the autoinhibition mechanism of the type III secretion system effectors of the NEL family.
Authors: Zouhir, S. / Bernal-Bayard, J. / Cordero-Alba, M. / Cardenal-Munoz, E. / Guimaraes, B. / Lazar, N. / Ramos-Morales, F. / Nessler, S.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SlrP
B: E3 ubiquitin-protein ligase SlrP
C: Thioredoxin
D: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)172,2474
Polymers172,2474
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-27 kcal/mol
Surface area69210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.290, 134.830, 154.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase SlrP / Secreted effector protein SlrP


Mass: 72967.562 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 141-765
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 14028 / Gene: slrP, STM14_928 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15/pREP4
References: UniProt: D0ZRB2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Thioredoxin / Trx / ATL-derived factor / ADF / Surface-associated sulphydryl protein / SASP


Mass: 13156.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXN, TRDX, TRX, TRX1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15/pREP4 / References: UniProt: P10599

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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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.8
Details: 15% PEG 4000, 0.2M NaCl, 0.1M MgCl2, 0.1M Hepes, 216 M SlrP, 430 M Trx1, pH 7.8, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979138 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelengthWavelength: 0.979138 Å / Relative weight: 1
ReflectionResolution: 3.296→45 Å / Num. all: 34242 / Num. obs: 34042 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rsym value: 5.6 / Net I/σ(I): 16.84
Reflection shellResolution: 3.29→3.49 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.83 / Num. unique all: 5299 / Rsym value: 69.9 / % possible all: 98.1

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.296→43.854 Å / SU ML: 0.53 / Isotropic thermal model: isotropic / σ(F): 1.99 / Phase error: 38.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3084 1701 5.01 %random
Rwork0.2717 ---
obs0.2735 33974 99.28 %-
all-34022 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 118.53 Å2
Refinement stepCycle: LAST / Resolution: 3.296→43.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11382 0 0 0 11382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311608
X-RAY DIFFRACTIONf_angle_d0.78515743
X-RAY DIFFRACTIONf_dihedral_angle_d11.7364385
X-RAY DIFFRACTIONf_chiral_restr0.0491788
X-RAY DIFFRACTIONf_plane_restr0.0052053
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.2955-3.39250.47991340.43542544254496
3.3925-3.50190.4351410.393226652665100
3.5019-3.6270.42711400.355826512651100
3.627-3.77220.34911400.31382674267499
3.7722-3.94380.35911410.2892665266599
3.9438-4.15150.31081400.27426572657100
4.1515-4.41140.29451430.272526992699100
4.4114-4.75160.28141410.247226832683100
4.7516-5.22910.26081420.25242701270199
5.2291-5.98420.32271440.298827232723100
5.9842-7.53320.33541440.295627512751100
7.5332-43.85780.2551510.21692860286099

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