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- PDB-6ggr: Crystal structure of Salmonella zinc metalloprotease effector Gtg... -

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Basic information

Entry
Database: PDB / ID: 6ggr
TitleCrystal structure of Salmonella zinc metalloprotease effector GtgA in complex with p65
Components
  • Bacteriophage virulence determinant
  • Transcription factor p65
KeywordsMETAL BINDING PROTEIN / Protease / Metalloprotease / zinc
Function / homology
Function and homology information


SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation ...SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / TRAF6 mediated NF-kB activation / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation / positive regulation of chondrocyte differentiation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / acetaldehyde metabolic process / Downstream TCR signaling / prolactin signaling pathway / NF-kappaB p50/p65 complex / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / negative regulation of protein sumoylation / defense response to tumor cell / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / NF-kappaB complex / response to UV-B / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / response to cobalamin / positive regulation of T cell receptor signaling pathway / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / response to amino acid / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of interleukin-12 production / negative regulation of insulin receptor signaling pathway / negative regulation of angiogenesis / negative regulation of miRNA transcription / liver development / response to progesterone / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / peptide binding / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to bacterium / protein catabolic process / response to insulin / negative regulation of protein catabolic process / chromatin DNA binding / defense response / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to hydrogen peroxide / histone deacetylase binding / positive regulation of miRNA transcription / cellular response to nicotine / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / cellular response to tumor necrosis factor / chromatin organization / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / DNA-templated transcription
Similarity search - Function
PipA / PipA protein / Rel homology domain (RHD), DNA-binding domain / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain ...PipA / PipA protein / Rel homology domain (RHD), DNA-binding domain / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Bacteriophage virulence determinant / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsJennings, E. / Esposito, D. / Rittinger, K. / Thurston, T.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001142 United Kingdom
Imperial College LondonRSRO_P50016 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/R011834/1 United Kingdom
Wellcome Trust102410/Z/13/ZR United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure-function analyses of the bacterial zinc metalloprotease effector protein GtgA uncover key residues required for deactivating NF-kappa B.
Authors: Jennings, E. / Esposito, D. / Rittinger, K. / Thurston, T.L.M.
History
DepositionMay 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 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
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: Transcription factor p65
B: Bacteriophage virulence determinant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4864
Polymers43,4152
Non-polymers712
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-29 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.392, 85.833, 111.869
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 Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3


Mass: 19316.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rela, Nfkb3 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q04207
#2: Protein Bacteriophage virulence determinant


Mass: 24098.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Gene: gtgA, STM14_1166 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0F6AZI6
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystallyzation conditions: 0.1 M Tris pH 8.3, 0.5 M LiCl and 32.5% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.097→55.93 Å / Num. obs: 22948 / % possible obs: 99.03 % / Redundancy: 31.1 % / Rmerge(I) obs: 0.1894 / Rpim(I) all: 0.03482 / Rrim(I) all: 0.1927 / Net I/σ(I): 13.9
Reflection shellResolution: 2.097→2.172 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RAM

2ram


Resolution: 2.097→55.93 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.84
RfactorNum. reflection% reflection
Rfree0.252 1129 4.96 %
Rwork0.2061 --
obs0.2084 22771 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.097→55.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 2 149 3028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062943
X-RAY DIFFRACTIONf_angle_d0.6453997
X-RAY DIFFRACTIONf_dihedral_angle_d17.3371124
X-RAY DIFFRACTIONf_chiral_restr0.052429
X-RAY DIFFRACTIONf_plane_restr0.004542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0974-2.19290.32891340.2842648X-RAY DIFFRACTION98
2.1929-2.30850.33661400.28792552X-RAY DIFFRACTION96
2.3085-2.45310.28221370.25512688X-RAY DIFFRACTION100
2.4531-2.64250.33311390.24122685X-RAY DIFFRACTION100
2.6425-2.90840.25831380.23312673X-RAY DIFFRACTION99
2.9084-3.32930.24611590.20762732X-RAY DIFFRACTION100
3.3293-4.19450.25321360.17652754X-RAY DIFFRACTION100
4.1945-55.930.19641460.1752910X-RAY DIFFRACTION100

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