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- PDB-7lew: Crystal structure of UBE2G2 in complex with the UBE2G2-binding re... -

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Basic information

Entry
Database: PDB / ID: 7lew
TitleCrystal structure of UBE2G2 in complex with the UBE2G2-binding region of AUP1
Components
  • Lipid droplet-regulating VLDL assembly factor AUP1
  • Ubiquitin-conjugating enzyme E2 G2
KeywordsLIGASE/Transferase / alpha beta / LIGASE / LIGASE-Transferase complex
Function / homology
Function and homology information


lipophagy / negative regulation of retrograde protein transport, ER to cytosol / lipid droplet formation / lipid droplet organization / ubiquitin conjugating enzyme binding / retrograde protein transport, ER to cytosol / protein localization to lipid droplet / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination ...lipophagy / negative regulation of retrograde protein transport, ER to cytosol / lipid droplet formation / lipid droplet organization / ubiquitin conjugating enzyme binding / retrograde protein transport, ER to cytosol / protein localization to lipid droplet / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / cellular response to interferon-beta / ERAD pathway / lipid droplet / autophagosome / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / response to virus / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / ubiquitin protein ligase binding / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular exosome / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
: / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme ...: / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / : / 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 / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 G2 / Lipid droplet-regulating VLDL assembly factor AUP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.736 Å
AuthorsLiang, Y.-H. / Smith, C.E. / Tsai, Y.C. / Weissman, A.M. / Ji, X.
Citation
Journal: Plos Biol. / Year: 2021
Title: A structurally conserved site in AUP1 binds the E2 enzyme UBE2G2 and is essential for ER-associated degradation.
Authors: Smith, C.E. / Tsai, Y.C. / Liang, Y.H. / Khago, D. / Mariano, J. / Li, J. / Tarasov, S.G. / Gergel, E. / Tsai, B. / Villaneuva, M. / Clapp, M.E. / Magidson, V. / Chari, R. / Byrd, R.A. / Ji, X. / Weissman, A.M.
#1: Journal: Mol Cell / Year: 2009
Title: Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78.
Authors: Das, R. / Mariano, J. / Tsai, Y.C. / Kalathur, R.C. / Kostova, Z. / Li, J. / Tarasov, S.G. / McFeeters, R.L. / Altieri, A.S. / Ji, X. / Byrd, R.A. / Weissman, A.M.
History
DepositionJan 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 G2
B: Lipid droplet-regulating VLDL assembly factor AUP1


Theoretical massNumber of molelcules
Total (without water)22,7742
Polymers22,7742
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-11 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.739, 58.226, 63.392
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 G2 / E2 ubiquitin-conjugating enzyme G2 / Ubiquitin carrier protein G2 / Ubiquitin-protein ligase G2


Mass: 18582.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G2, UBC7 / Plasmid: pETDuet-GST / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P60604, E2 ubiquitin-conjugating enzyme
#2: Protein/peptide Lipid droplet-regulating VLDL assembly factor AUP1 / Ancient ubiquitous protein 1


Mass: 4191.585 Da / Num. of mol.: 1 / Fragment: UBE2G2-binding region (G2BR) of AUP1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AUP1 / Plasmid: pETDuet-GST / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y679
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Description: rod-shaped crystals of dimensions 0.08 mm x 0.08 mm x 0.3 mm
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4000, ammonium acetate etc.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 19, 2011 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.736→50 Å / Num. obs: 19573 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 25.15 Å2 / Rmerge(I) obs: 0.034 / Χ2: 1.024 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.736-1.85.60.50219171.049199.5
1.8-1.875.70.32319311.007199.5
1.87-1.965.20.22119061.038199.5
1.96-2.065.70.13719331.043199.8
2.06-2.195.70.09519361.014199.7
2.19-2.364.90.07419441.041199.9
2.36-2.65.70.04819501.019199.9
2.6-2.985.70.03119750.9991100
2.98-3.755.30.02219870.999199.7
3.75-5050.01820941.033198.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H8K

3h8k


Resolution: 1.736→37.819 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1003 5.14 %
Rwork0.1915 18524 -
obs0.1934 19527 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.06 Å2 / Biso mean: 36.2691 Å2 / Biso min: 15.05 Å2
Refinement stepCycle: final / Resolution: 1.736→37.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 0 160 1630
Biso mean---38.49 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111560
X-RAY DIFFRACTIONf_angle_d1.1162122
X-RAY DIFFRACTIONf_chiral_restr0.062220
X-RAY DIFFRACTIONf_plane_restr0.009282
X-RAY DIFFRACTIONf_dihedral_angle_d12.827973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7363-1.82780.30521350.2477259398
1.8278-1.94230.29211460.23222578100
1.9423-2.09230.25521360.21122617100
2.0923-2.30280.25641500.19762631100
2.3028-2.6360.24221410.19842658100
2.636-3.32070.22951400.18472689100
3.3207-37.8190.1951550.1774275899

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