[English] 日本語
Yorodumi
- PDB-6ggr: Crystal structure of Salmonella zinc metalloprotease effector Gtg... -

+
Open data


ID or keywords:

Loading...

-
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 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / prolactin signaling pathway / Downstream TCR signaling / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / response to cobalamin / cellular response to peptidoglycan / ankyrin repeat binding / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / defense response to tumor cell / cellular response to interleukin-6 / actinin binding / response to UV-B / non-canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / NF-kappaB complex / signal transduction involved in regulation of gene expression / 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 / phosphate ion binding / positive regulation of T cell receptor signaling pathway / cellular response to lipoteichoic acid / response to muramyl dipeptide / positive regulation of vascular endothelial growth factor production / cellular response to angiotensin / general transcription initiation factor binding / response to cAMP / canonical NF-kappaB signal transduction / hair follicle development / NF-kappaB binding / neuropeptide signaling pathway / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / response to muscle stretch / positive regulation of interleukin-12 production / antiviral innate immune response / negative regulation of cytokine production involved in inflammatory response / peptide binding / negative regulation of insulin receptor signaling pathway / response to progesterone / negative regulation of miRNA transcription / negative regulation of angiogenesis / animal organ morphogenesis / response to ischemia / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to bacterium / protein catabolic process / liver development / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / defense response / response to insulin / negative regulation of protein catabolic process / chromatin DNA binding / cellular response to nicotine / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / histone deacetylase binding / cellular response to hydrogen peroxide / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / chromatin organization / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / inflammatory response
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more