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- PDB-4q5h: Shigella Effector Kinase OspG bound to AMPPNP and E2-Ub UbcH7-Ub ... -

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Basic information

Entry
Database: PDB / ID: 4q5h
TitleShigella Effector Kinase OspG bound to AMPPNP and 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Polyubiquitin / Ubiquitin-conjugating enzyme E2 L3 / Protein kinase OspG
Similarity search - Component
Biological speciesShigella sonnei (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.999 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 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,3435
Polymers46,8123
Non-polymers5312
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-29 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.416, 84.658, 85.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

#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 (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

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Non-polymers , 3 types, 232 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
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: 2→50 Å / Num. obs: 33962 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 35.08 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2-2.0371100
2.03-2.077.11100
2.07-2.117.211000.912
2.11-2.157.211000.831
2.15-2.27.211000.744
2.2-2.257.211000.552
2.25-2.317.211000.453
2.31-2.377.211000.379
2.37-2.447.211000.33
2.44-2.527.211000.282
2.52-2.617.211000.219
2.61-2.717.211000.181
2.71-2.847.211000.143
2.84-2.997.211000.112
2.99-3.177.211000.093
3.17-3.427.111000.085
3.42-3.767.111000.072
3.76-4.317.111000.058
4.31-5.43711000.052
5.43-506.5199.10.054

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 4QSE

4qse


Resolution: 1.999→44.939 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 1720 5.07 %
Rwork0.1903 --
obs0.1922 33903 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.66 Å2
Refinement stepCycle: LAST / Resolution: 1.999→44.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 32 230 3483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063393
X-RAY DIFFRACTIONf_angle_d0.9894618
X-RAY DIFFRACTIONf_dihedral_angle_d14.271327
X-RAY DIFFRACTIONf_chiral_restr0.04511
X-RAY DIFFRACTIONf_plane_restr0.004602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9992-2.0580.32881380.27242638X-RAY DIFFRACTION100
2.058-2.12440.27961400.23842643X-RAY DIFFRACTION100
2.1244-2.20040.29091460.24262643X-RAY DIFFRACTION100
2.2004-2.28850.28381390.21592645X-RAY DIFFRACTION100
2.2885-2.39260.27951420.21522645X-RAY DIFFRACTION100
2.3926-2.51880.24021510.21352661X-RAY DIFFRACTION100
2.5188-2.67650.2731340.20762673X-RAY DIFFRACTION100
2.6765-2.88320.24491510.21122665X-RAY DIFFRACTION100
2.8832-3.17320.24091440.20042687X-RAY DIFFRACTION100
3.1732-3.63220.20651340.18562712X-RAY DIFFRACTION100
3.6322-4.57550.18661620.15092710X-RAY DIFFRACTION100
4.5755-44.95060.20751390.1782861X-RAY DIFFRACTION99
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)
11.64550.4437-0.72122.6339-1.10832.354-0.07860.0522-0.1439-0.07130.0206-0.20170.15810.10310.02830.19790.02660.01720.1697-0.01950.211926.6285-55.2719-2.6563
20.5623-0.1338-0.09430.3598-0.18780.5412-0.0231-0.07260.03680.0552-0.039-0.0184-0.06530.01260.04270.34-0.0055-0.01250.3058-0.00210.285118.8893-45.5425-4.3037
34.06940.99080.56734.4875-0.50736.4406-0.05750.6260.5069-0.03940.0536-0.2831-0.64630.3590.01330.2886-0.04780.04250.29890.08750.341736.9555-34.5671-16.6533
41.276-0.886-0.33875.2083-2.16213.92320.0766-0.10910.19620.26310.0120.2661-0.768-0.182-0.03780.30360.0267-0.02680.2519-0.05550.24012.5482-31.0503-5.7098
53.9164-0.18732.25141.42952.00954.432-0.03030.248-0.1351-0.3315-0.1356-0.75410.27670.83660.28780.4640.03520.07620.43970.12790.514924.5339-60.9524-3.3554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 25:193 )A25 - 193
2X-RAY DIFFRACTION2( CHAIN A AND RESID 301:423 ) OR ( CHAIN C AND RESID 201:288 ) OR ( CHAIN B AND RESID 101:119 )A301 - 423
3X-RAY DIFFRACTION2( CHAIN A AND RESID 301:423 ) OR ( CHAIN C AND RESID 201:288 ) OR ( CHAIN B AND RESID 101:119 )C201 - 288
4X-RAY DIFFRACTION2( CHAIN A AND RESID 301:423 ) OR ( CHAIN C AND RESID 201:288 ) OR ( CHAIN B AND RESID 101:119 )B101 - 119
5X-RAY DIFFRACTION3( CHAIN B AND RESID 1:76 )B1 - 76
6X-RAY DIFFRACTION4( CHAIN C AND RESID 0:154 )C0 - 154
7X-RAY DIFFRACTION5( CHAIN A AND RESID 202:202 )A202

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