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- PDB-4wz3: Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box... -

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Basic information

Entry
Database: PDB / ID: 4wz3
TitleCrystal structure of the complex between LubX/LegU2/Lpp2887 U-box 1 and Homo sapiens UBE2D2
Components
  • E3 ubiquitin-protein ligase LubX
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / alpha/beta protein / effector / activating enzyme / structural genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / protein quality control for misfolded or incompletely synthesized proteins / ubiquitin conjugating enzyme activity / positive regulation of proteolysis / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment ...(E3-independent) E2 ubiquitin-conjugating enzyme / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / protein quality control for misfolded or incompletely synthesized proteins / ubiquitin conjugating enzyme activity / positive regulation of proteolysis / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / host cell / protein-folding chaperone binding / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 ...U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase LubX
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsStogios, P.J. / Quaile, A.T. / Skarina, T. / Nocek, B. / Di Leo, R. / Yim, V. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Structure / Year: 2015
Title: Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila.
Authors: Quaile, A.T. / Urbanus, M.L. / Stogios, P.J. / Nocek, B. / Skarina, T. / Ensminger, A.W. / Savchenko, A.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Aug 19, 2015Group: Derived calculations
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.8Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
B: E3 ubiquitin-protein ligase LubX


Theoretical massNumber of molelcules
Total (without water)41,6142
Polymers41,6142
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.293, 119.293, 49.809
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating ...Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 16796.213 Da / Num. of mol.: 1 / Mutation: C85S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62837, ubiquitin-protein ligase
#2: Protein E3 ubiquitin-protein ligase LubX / Legionella U-box protein


Mass: 24818.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Paris / Gene: lubX, lpp2887 / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5X159, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15 mg/ml of E2D2.(C85S)-Ub conjugate and an equimolar concentration of LubX (1-186), 0.2 M sodium tartrate, 0.1 M Tris-Cl (pH 8.5) and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789897 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789897 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 11243 / % possible obs: 99 % / Redundancy: 5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.05
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 4.07 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIXphasing
PHENIXmodel building
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DDI, LubX U-box 1 WT PDB code 4WZ0

4ddi

4wz0


Resolution: 2.7→35.855 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 968 5.12 %Random selection
Rwork0.1668 ---
obs0.1697 10884 86.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→35.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 0 53 2706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052746
X-RAY DIFFRACTIONf_angle_d0.9033737
X-RAY DIFFRACTIONf_dihedral_angle_d13.8741055
X-RAY DIFFRACTIONf_chiral_restr0.044417
X-RAY DIFFRACTIONf_plane_restr0.007484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.84040.366870.24431563X-RAY DIFFRACTION53
2.8404-3.01830.28511280.23062170X-RAY DIFFRACTION74
3.0183-3.25120.28291580.21122699X-RAY DIFFRACTION91
3.2512-3.57810.231590.18312912X-RAY DIFFRACTION98
3.5781-4.09520.19591520.14672895X-RAY DIFFRACTION98
4.0952-5.1570.19641410.12832890X-RAY DIFFRACTION97
5.157-35.85840.17821430.15692805X-RAY DIFFRACTION95
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)
13.1131.65072.41433.2676-0.4043.09720.2494-1.0676-0.39330.4166-0.1271-0.8479-0.5462-0.1519-0.07970.37130.02160.09030.47760.11340.5333-36.044713.407210.1917
28.74456.0095-5.49118.3195-6.69328.2605-0.1546-1.3015-0.786-0.4905-0.248-1.28970.69951.49690.21970.2786-0.0109-0.10120.39680.060.4997-42.67814.199311.3687
35.78452.5585-0.81164.6928-2.46422.11080.0647-0.06430.05720.119-0.03050.075-0.2893-0.3685-0.03640.21620.0425-0.01270.2492-0.02860.1197-53.85999.52988.8761
46.4539-3.27740.56697.7887-1.59712.8351-0.0514-0.8599-0.76630.71470.28221.1747-0.4717-0.351-0.19570.2474-0.0330.04030.46090.07450.3259-68.55123.130615.2142
53.10440.89091.54053.13850.56354.3426-0.17890.14930.352-0.30360.11310.14670.0174-0.24090.01410.239-0.03910.07620.22340.11870.2851-37.130531.90785.198
65.628-4.16116.6936.9491-7.30539.2877-0.0354-0.17280.151-0.1741-0.2681-0.25080.19770.02730.21230.24460.02930.09140.27640.04460.2757-11.165316.006520.9715
77.6716-4.1121-1.16783.15420.94861.17480.0454-0.7006-0.3261.16610.28460.7242-0.8705-0.2821-0.20990.78660.050.35060.47950.08890.5992-19.939214.711933.3483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 0:18
2X-RAY DIFFRACTION2chain A and resi 19:38
3X-RAY DIFFRACTION3chain A and resi 39:116
4X-RAY DIFFRACTION4chain A and resi 117:147
5X-RAY DIFFRACTION5chain B and resi 4:94
6X-RAY DIFFRACTION6chain B and resi 95:122
7X-RAY DIFFRACTION7chain B and resi 123:186

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