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- PDB-3w31: Structual basis for the recognition of Ubc13 by the Shigella flex... -

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Basic information

Entry
Database: PDB / ID: 3w31
TitleStructual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI
Components
  • ORF169b
  • Ubiquitin-conjugating enzyme E2 N
KeywordsIMMUNE SYSTEM / Type 3 secretion system / Effector / Deamidation
Function / homology
Function and homology information


UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / regulation protein catabolic process at postsynapse / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction / E2 ubiquitin-conjugating enzyme ...UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / regulation protein catabolic process at postsynapse / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / regulation of DNA repair / negative regulation of TORC1 signaling / antiviral innate immune response / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of DNA repair / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / ubiquitin binding / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / TAK1-dependent IKK and NF-kappa-B activation / double-strand break repair via homologous recombination / NOD1/2 Signaling Pathway / G2/M DNA damage checkpoint / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Aggrephagy / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / T cell receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / Processing of DNA double-strand break ends / positive regulation of canonical NF-kappaB signal transduction / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynapse / protein ubiquitination / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / glutamatergic synapse / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cathepsin B; Chain A - #140 / : / : / Shigella glutamine deamidase OspI / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme ...Cathepsin B; Chain A - #140 / : / : / Shigella glutamine deamidase OspI / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Cathepsin B; Chain A / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Ubiquitin-conjugating enzyme E2 N / ORF169b
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsNishide, A. / Kim, M. / Takagi, K. / Sasakawa, C. / Mizushima, T.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural basis for the recognition of Ubc13 by the Shigella flexneri effector OspI.
Authors: Nishide, A. / Kim, M. / Takagi, K. / Himeno, A. / Sanada, T. / Sasakawa, C. / Mizushima, T.
History
DepositionDec 7, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF169b
B: Ubiquitin-conjugating enzyme E2 N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0666
Polymers41,5592
Non-polymers5084
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-8 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.238, 119.238, 69.985
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein ORF169b


Mass: 24118.807 Da / Num. of mol.: 1 / Mutation: C62A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ORF169b, CP0209 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VSD5
#2: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / Ubc13 / UbcH13 / Ubiquitin carrier protein N / ...Bendless-like ubiquitin-conjugating enzyme / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17440.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli) / References: UniProt: P61088, ubiquitin-protein ligase
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.4M potassium iodide, 0.1M MES (pH6.5), 4mM DTT, 15% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorDate: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. all: 12250 / Num. obs: 12193 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.094

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B21, 1JBB

3b21

1jbb


Resolution: 2.96→33.1 Å
RfactorNum. reflection
Rfree0.284 1251
Rwork0.245 -
all-12256
obs-12150
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.685 Å20 Å20 Å2
2--0.685 Å20 Å2
3----1.369 Å2
Refinement stepCycle: LAST / Resolution: 2.96→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 4 0 2703

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