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- PDB-3sy2: Crystal structure of the Salmonella E3 ubiquitin ligase SopA in c... -

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Basic information

Entry
Database: PDB / ID: 3sy2
TitleCrystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7
Components
  • E3 ubiquitin-protein ligase SopA
  • Ubiquitin-conjugating enzyme E2 L3
KeywordsLIGASE/SIGNALING PROTEIN / pentapeptide / HECT domain / HECT E3 / HECT E3 ubiquitin ligase / E2 ubiquitin conjugating enzyme / ubiquitin / protein-protein complex / effector protein / ubiquitin transfer / ubiquitination / LIGASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


cell cycle phase transition / ubiquitin-protein transferase activator activity / HECT-type E3 ubiquitin transferase / protein K11-linked ubiquitination / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / cellular response to glucocorticoid stimulus / cellular response to steroid hormone stimulus / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity ...cell cycle phase transition / ubiquitin-protein transferase activator activity / HECT-type E3 ubiquitin transferase / protein K11-linked ubiquitination / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / cellular response to glucocorticoid stimulus / cellular response to steroid hormone stimulus / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / PINK1-PRKN Mediated Mitophagy / positive regulation of protein ubiquitination / Regulation of TNFR1 signaling / protein modification process / Regulation of necroptotic cell death / protein polyubiquitination / ubiquitin-protein transferase activity / host cell / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / presynapse / ubiquitin-dependent protein catabolic process / cell population proliferation / transcription coactivator activity / protein ubiquitination / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / RNA binding / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
effector protein (NleL) fold / effector protein (NleL) / Putative secreted effector protein / HECT-like ubiquitin ligase fold / HECT-like ubiquitin ligase / E3 ubiquitin ligase SopA-like central domain / SopA-like central domain / E3 ubiquitin-protein ligase SopA-like, catalytic domain / SopA-like, catalytic domain superfamily / SopA-like catalytic domain ...effector protein (NleL) fold / effector protein (NleL) / Putative secreted effector protein / HECT-like ubiquitin ligase fold / HECT-like ubiquitin ligase / E3 ubiquitin ligase SopA-like central domain / SopA-like central domain / E3 ubiquitin-protein ligase SopA-like, catalytic domain / SopA-like, catalytic domain superfamily / SopA-like catalytic domain / E3 ubiquitin-protein ligase SopA / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Pectate Lyase C-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / 3 Solenoid / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Roll / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 L3 / E3 ubiquitin-protein ligase SopA
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsDiao, J. / Lin, D.Y. / Chen, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions.
Authors: Lin, D.Y. / Diao, J. / Chen, J.
History
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Sep 13, 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 / 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 / _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: E3 ubiquitin-protein ligase SopA
B: E3 ubiquitin-protein ligase SopA
C: Ubiquitin-conjugating enzyme E2 L3
D: Ubiquitin-conjugating enzyme E2 L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,6345
Polymers174,5384
Non-polymers961
Water27015
1
A: E3 ubiquitin-protein ligase SopA
D: Ubiquitin-conjugating enzyme E2 L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3653
Polymers87,2692
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase SopA
C: Ubiquitin-conjugating enzyme E2 L3


Theoretical massNumber of molelcules
Total (without water)87,2692
Polymers87,2692
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.120, 118.363, 241.671
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 E3 ubiquitin-protein ligase SopA / Salmonella outer protein A / Secreted effector protein SopA


Mass: 69235.219 Da / Num. of mol.: 2
Fragment: C-terminal beta-helix domain and HECT-like domain (UNP residues 165-782)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: sopA, STM2066 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star
References: UniProt: Q8ZNR3, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: 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: 18033.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L3, UBCE7, UBCH7 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: P68036, ubiquitin-protein ligase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 1.6 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03324 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 31621 / Num. obs: 31621 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 85.18 Å2 / Rsym value: 0.147 / Net I/σ(I): 7.19
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.39 / Num. unique all: 3105 / Rsym value: 0.52 / % possible all: 83.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2QYU AND 1C4Z

2qyu

1c4z


Resolution: 3.27→45.424 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 1571 4.97 %RANDOM
Rwork0.2112 ---
obs0.2144 31609 93.76 %-
all-31621 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.369 Å2 / ksol: 0.307 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5143 Å20 Å20 Å2
2---3.8234 Å2-0 Å2
3---2.309 Å2
Refinement stepCycle: LAST / Resolution: 3.27→45.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11640 0 5 15 11660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511949
X-RAY DIFFRACTIONf_angle_d0.86416328
X-RAY DIFFRACTIONf_dihedral_angle_d14.7674174
X-RAY DIFFRACTIONf_chiral_restr0.0591846
X-RAY DIFFRACTIONf_plane_restr0.0042138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2702-3.37580.39631120.30062268X-RAY DIFFRACTION79
3.3758-3.49640.35671470.27682728X-RAY DIFFRACTION96
3.4964-3.63630.34571490.25722770X-RAY DIFFRACTION97
3.6363-3.80170.32821510.22972775X-RAY DIFFRACTION97
3.8017-4.0020.25671530.22192791X-RAY DIFFRACTION97
4.002-4.25260.25631390.19362758X-RAY DIFFRACTION96
4.2526-4.58070.25021470.17222768X-RAY DIFFRACTION95
4.5807-5.04110.23051410.17082757X-RAY DIFFRACTION95
5.0411-5.76930.2791460.21782802X-RAY DIFFRACTION95
5.7693-7.26390.33171520.23812799X-RAY DIFFRACTION95
7.2639-45.42790.21691340.19072822X-RAY DIFFRACTION90
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)
10.61380.48890.23350.6145-0.5554-0.10340.1743-0.0817-0.07520.2859-0.2529-0.0497-0.2069-0.20710.01160.5077-0.0591-0.00050.41680.01290.324911.6185-27.18960.9426
20.712-0.1105-0.09690.6810.1740.02280.1213-0.0047-0.1062-0.1668-0.1032-0.0554-0.092-0.0208-0.02140.51350.00320.02780.4479-0.02180.451-15.50876.3897-10.7901
30.04970.0129-0.00570.08870.01280.2711-0.1399-0.02190.10310.00760.07040.00630.02620.18350.05980.3102-0.04220.0050.40760.10610.4821-27.9237-27.981436.3258
40.1823-0.0985-0.00490.0467-0.09450.2027-0.0684-0.01010.1484-0.014-0.1129-0.0842-0.01430.07910.0990.5177-0.06310.0130.59450.06040.597924.4344-13.34694.7809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 168:782)
2X-RAY DIFFRACTION2(chain B and resid 165:782)
3X-RAY DIFFRACTION3(chain C and resid 1:154)
4X-RAY DIFFRACTION4(chain D and resid 1:154)

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