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- PDB-4q5e: Shigella Effector Kinase OspG bound to E2-Ub UbcH7-Ub Conjugate -

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Basic information

Entry
Database: PDB / ID: 4q5e
TitleShigella Effector Kinase OspG bound to E2-Ub UbcH7-Ub Conjugate
Components
  • Polyubiquitin
  • Protein kinase OspG
  • Ubiquitin-conjugating enzyme E2 L3
KeywordsUNKNOWN FUNCTION / PROTEIN BINDING / protein-protein complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / kinase fold / inhibition of NF-kB pathway
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / host cell / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus ...Transferases; Transferring phosphorus-containing groups / cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / host cell / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / Regulation of TNFR1 signaling / protein modification process / modification-dependent protein catabolic process / Regulation of necroptotic cell death / protein tag activity / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / kinase activity / ubiquitin-dependent protein catabolic process / cell population proliferation / protein autophosphorylation / transcription coactivator activity / protein ubiquitination / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / extracellular space / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin conserved site ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Roll / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin / Ubiquitin-conjugating enzyme E2 L3 / Protein kinase OspG
Similarity search - Component
Biological speciesShigella sonnei Ss046 (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.869 Å
AuthorsCygler, M. / Grishin, A.M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Structure / Year: 2014
Title: Structural Basis for the Inhibition of Host Protein Ubiquitination by Shigella Effector Kinase OspG.
Authors: Grishin, A.M. / Condos, T.E. / Barber, K.R. / Campbell-Valois, F.X. / Parsot, C. / Shaw, G.S. / Cygler, M.
History
DepositionApr 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase OspG
B: Polyubiquitin
C: Ubiquitin-conjugating enzyme E2 L3


Theoretical massNumber of molelcules
Total (without water)46,8123
Polymers46,8123
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-15 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.312, 84.141, 85.367
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 Protein kinase OspG / Effector protein OspG


Mass: 20116.547 Da / Num. of mol.: 1 / Fragment: unp residues 26-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella sonnei Ss046 (bacteria) / Strain: 2457T / Gene: ospG, SSON_P170 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
References: UniProt: Q3YTH2, Transferases; Transferring phosphorus-containing groups
#2: Protein Polyubiquitin / Ubiquitin


Mass: 8642.873 Da / Num. of mol.: 1 / Mutation: C17S, C137S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SCD2, UBE2L3, UBI4, YLL039C / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG63, ubiquitin-protein ligase
#3: Protein Ubiquitin-conjugating enzyme E2 L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin- ...L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin-protein ligase L3


Mass: 18052.662 Da / Num. of mol.: 1 / Mutation: K48R, G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBCE7, UBCH7, UBE2L3, UBI4 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P68036, ubiquitin-protein ligase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Hepes 8.2, 15% PEG 4000, 100 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 13, 2013
RadiationMonochromator: dcm WITH CRYO-COOLED 1ST CRYSTAL SAGITALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 40758 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 36.84 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
1.87-1.911.11100
1.9-1.9411.11100
1.94-1.9711.111000.95
1.97-2.0111.211000.782
2.01-2.0611.111000.64
2.06-2.1111.111000.501
2.11-2.1611.211000.483
2.16-2.2211.111000.362
2.22-2.2811.211000.276
2.28-2.3611.111000.228
2.36-2.4411.211000.206
2.44-2.5411.111000.175
2.54-2.6511.111000.15
2.65-2.791111000.135
2.79-2.9711.111000.119
2.97-3.21111000.102
3.2-3.521111000.091
3.52-4.0310.911000.084
4.03-5.0710.811000.077
5.07-5010.1199.40.076

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.98
Highest resolutionLowest resolution
Rotation2.5 Å44.76 Å
Translation2.5 Å44.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.869→44.758 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 2044 5.02 %
Rwork0.1846 --
obs0.1869 40691 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.09 Å2
Refinement stepCycle: LAST / Resolution: 1.869→44.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 0 237 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143326
X-RAY DIFFRACTIONf_angle_d1.4654509
X-RAY DIFFRACTIONf_dihedral_angle_d14.0451290
X-RAY DIFFRACTIONf_chiral_restr0.071498
X-RAY DIFFRACTIONf_plane_restr0.007592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8686-1.91210.31791150.2772425X-RAY DIFFRACTION95
1.9121-1.95990.28961410.24562548X-RAY DIFFRACTION100
1.9599-2.01290.29721590.22352495X-RAY DIFFRACTION100
2.0129-2.07210.23411230.21462572X-RAY DIFFRACTION100
2.0721-2.1390.23911470.20172549X-RAY DIFFRACTION100
2.139-2.21550.22561480.20152558X-RAY DIFFRACTION100
2.2155-2.30420.22941280.18522565X-RAY DIFFRACTION100
2.3042-2.4090.25471360.19642577X-RAY DIFFRACTION100
2.409-2.5360.25211450.19492542X-RAY DIFFRACTION100
2.536-2.69490.2431360.19412599X-RAY DIFFRACTION100
2.6949-2.90290.28231340.20462574X-RAY DIFFRACTION100
2.9029-3.1950.22051290.19452609X-RAY DIFFRACTION100
3.195-3.65710.22361150.1772630X-RAY DIFFRACTION100
3.6571-4.60690.19121410.15252642X-RAY DIFFRACTION100
4.6069-44.77110.23681470.18382762X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.86940.1351-0.87352.6196-1.10032.317-0.06010.0315-0.12420.03720.0582-0.11280.15890.0777-0.00790.22790.03290.00950.2266-0.0120.232826.6417-54.9165-2.6054
23.53160.62060.47544.0551-0.34876.09640.00640.46380.65570.03980.1194-0.1301-0.6030.0976-0.16460.3529-0.0090.07990.31120.10370.417737.019-34.1873-16.4966
31.4169-0.65840.00625.0821-2.15784.25980.0028-0.10230.18140.2770.03420.2436-0.74-0.2517-0.02320.35140.0456-0.03880.3452-0.05910.27722.5504-30.7163-5.6469
40.5118-0.43860.12710.3805-0.26230.6543-0.0757-0.07380.04560.08020.04350.004-0.0334-0.08570.02710.38110.0006-0.0010.37820.00780.296119.1926-45.446-3.4114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 26:193 )A26 - 193
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:76 )B1 - 76
3X-RAY DIFFRACTION3( CHAIN C AND RESID 0:154 )C0 - 154
4X-RAY DIFFRACTION4( CHAIN A AND RESID 201:324 ) OR ( CHAIN C AND RESID 201:289 ) OR ( CHAIN B AND RESID 101:124 )A201 - 324
5X-RAY DIFFRACTION4( CHAIN A AND RESID 201:324 ) OR ( CHAIN C AND RESID 201:289 ) OR ( CHAIN B AND RESID 101:124 )C201 - 289
6X-RAY DIFFRACTION4( CHAIN A AND RESID 201:324 ) OR ( CHAIN C AND RESID 201:289 ) OR ( CHAIN B AND RESID 101:124 )B101 - 124

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