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- PDB-6ac0: Crystal structure of TRADD death domain GlcNAcylated by EPEC effe... -

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Basic information

Entry
Database: PDB / ID: 6ac0
TitleCrystal structure of TRADD death domain GlcNAcylated by EPEC effector NleB
ComponentsTumor necrosis factor receptor type 1-associated DEATH domain protein
KeywordsSIGNALING PROTEIN / apoptosis
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily complex / death domain binding / Defective RIPK1-mediated regulated necrosis / positive regulation of hair follicle development / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / death-inducing signaling complex ...tumor necrosis factor receptor superfamily complex / death domain binding / Defective RIPK1-mediated regulated necrosis / positive regulation of hair follicle development / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / death-inducing signaling complex / transmembrane receptor protein tyrosine kinase adaptor activity / tumor necrosis factor receptor binding / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / extrinsic apoptotic signaling pathway via death domain receptors / canonical NF-kappaB signal transduction / extrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / kinase binding / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / cytoskeleton / receptor complex / positive regulation of cell migration / positive regulation of apoptotic process / apoptotic process / protein-containing complex binding / signal transduction / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor type 1-associated DEATH domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å
AuthorsDing, J. / Shao, F.
CitationJournal: Mol.Cell / Year: 2019
Title: Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector.
Authors: Ding, J. / Pan, X. / Du, L. / Yao, Q. / Xue, J. / Yao, H. / Wang, D.C. / Li, S. / Shao, F.
History
DepositionJul 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Tumor necrosis factor receptor type 1-associated DEATH domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5462
Polymers13,3251
Non-polymers2211
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.600, 28.600, 264.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Tumor necrosis factor receptor type 1-associated DEATH domain protein / TNFR1-associated DEATH domain protein / TNFRSF1A-associated via death domain


Mass: 13325.075 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRADD / Plasmid: pGEX6p / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15628
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.6 M Na/KPO4, pH 6.0

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.449→28.6 Å / Num. obs: 20061 / % possible obs: 96.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.1
Reflection shellResolution: 1.449→1.53 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2913 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OQ9

3oq9


Resolution: 1.449→28.435 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.2242 1022 5.1 %
Rwork0.1844 --
obs0.1864 20047 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.449→28.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 14 104 1037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006958
X-RAY DIFFRACTIONf_angle_d0.8731296
X-RAY DIFFRACTIONf_dihedral_angle_d20.633374
X-RAY DIFFRACTIONf_chiral_restr0.066143
X-RAY DIFFRACTIONf_plane_restr0.004174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.449-1.52540.26931520.20352694X-RAY DIFFRACTION99
1.5254-1.6210.21861440.16482750X-RAY DIFFRACTION99
1.621-1.74610.22711550.16922732X-RAY DIFFRACTION99
1.7461-1.92180.25221430.17332762X-RAY DIFFRACTION98
1.9218-2.19980.23291620.16572727X-RAY DIFFRACTION96
2.1998-2.77110.20091410.1872677X-RAY DIFFRACTION93
2.7711-28.440.22161250.19822683X-RAY DIFFRACTION85

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