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- PDB-9lhj: UBE2N/UBE2V2 complexed with a covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 9lhj
TitleUBE2N/UBE2V2 complexed with a covalent inhibitor
Components
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin-conjugating enzyme E2 variant 2
KeywordsLIGASE / Covalent inhibitor
Function / homology
Function and homology information


error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity ...error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / regulation of DNA repair / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of TORC1 signaling / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / antiviral innate immune response / activated TAK1 mediates p38 MAPK activation / positive regulation of DNA repair / ubiquitin binding / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / double-strand break repair via homologous recombination / Nonhomologous End-Joining (NHEJ) / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / Formation of Incision Complex in GG-NER / positive regulation of NF-kappaB transcription factor activity / G2/M DNA damage checkpoint / FCERI mediated NF-kB activation / Interleukin-1 signaling / Aggrephagy / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / T cell receptor signaling pathway / Processing of DNA double-strand break ends / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 N / Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLi, S. / Wu, X. / Zhou, L. / Lu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077019 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Proteome-Wide Data Guides the Discovery of Lysine-Targeting Covalent Inhibitors Using DNA-Encoded Chemical Libraries.
Authors: Wu, X. / Li, S. / Liang, T. / Yu, Q. / Zhang, Y. / Liu, J. / Li, K. / Liu, Z. / Cui, M. / Zhao, Y. / Han, X. / Jin, R. / Tan, M. / Chen, X.H. / Zhao, Y. / Zheng, M. / Sun, Y. / Zhou, L. / Lu, X.
History
DepositionJan 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Refinement description / Category: citation / software / Item: _citation.journal_volume / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 N
B: Ubiquitin-conjugating enzyme E2 N
C: Ubiquitin-conjugating enzyme E2 variant 2
D: Ubiquitin-conjugating enzyme E2 variant 2


Theoretical massNumber of molelcules
Total (without water)68,1264
Polymers68,1264
Non-polymers00
Water10,665592
1
A: Ubiquitin-conjugating enzyme E2 N

D: Ubiquitin-conjugating enzyme E2 variant 2


Theoretical massNumber of molelcules
Total (without water)34,0632
Polymers34,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1560 Å2
ΔGint-9 kcal/mol
Surface area15020 Å2
MethodPISA
2
B: Ubiquitin-conjugating enzyme E2 N

C: Ubiquitin-conjugating enzyme E2 variant 2


Theoretical massNumber of molelcules
Total (without water)34,0632
Polymers34,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area1230 Å2
ΔGint-10 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.415, 71.603, 68.560
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17682.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin-conjugating enzyme E2 variant 2 / DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation- ...DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation-promoting factor 1 / EDPF-1 / MMS2 homolog / Vitamin D3-inducible protein


Mass: 16380.731 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V2, MMS2, UEV2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15819
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BIS-TRIS pH 6.5, 20% w/v PEG 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.96183 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96183 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 68847 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Χ2: 0.657 / Net I/σ(I): 4 / Num. measured all: 455503
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.68-1.745.90.65268540.7840.9380.2920.7160.48899.9
1.74-1.816.60.57168260.8770.9670.2390.620.505100
1.81-1.896.70.44868830.9250.980.1850.4860.54100
1.89-1.996.60.34268270.9490.9870.1430.3710.594100
1.99-2.126.60.2568630.9690.9920.1040.2710.658100
2.12-2.286.90.18768660.9810.9950.0750.2010.714100
2.28-2.516.70.14268910.9860.9970.0590.1540.733100
2.51-2.876.80.10968990.9920.9980.0440.1180.723100
2.87-3.626.80.07869070.9940.9990.0320.0850.778100
3.62-506.50.06270310.9960.9990.0260.0670.806100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→35.8 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 3640 5.29 %
Rwork0.1824 --
obs0.1847 68806 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4609 0 0 592 5201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084784
X-RAY DIFFRACTIONf_angle_d1.0096500
X-RAY DIFFRACTIONf_dihedral_angle_d11.62652
X-RAY DIFFRACTIONf_chiral_restr0.062692
X-RAY DIFFRACTIONf_plane_restr0.01850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.28771190.22832449X-RAY DIFFRACTION97
1.7-1.720.28941500.22422465X-RAY DIFFRACTION100
1.72-1.750.27521230.22422522X-RAY DIFFRACTION100
1.75-1.770.30891450.23112497X-RAY DIFFRACTION100
1.77-1.80.26391480.22882499X-RAY DIFFRACTION100
1.8-1.830.30711710.24432453X-RAY DIFFRACTION100
1.83-1.860.26191490.21752500X-RAY DIFFRACTION100
1.86-1.90.24661260.19952496X-RAY DIFFRACTION100
1.9-1.930.23991650.20112450X-RAY DIFFRACTION100
1.93-1.970.26271220.1952525X-RAY DIFFRACTION100
1.97-2.020.26281670.1932519X-RAY DIFFRACTION100
2.02-2.060.25151650.18862457X-RAY DIFFRACTION100
2.06-2.120.19511390.18992488X-RAY DIFFRACTION100
2.12-2.170.26041200.19272545X-RAY DIFFRACTION100
2.17-2.240.23871340.19082491X-RAY DIFFRACTION100
2.24-2.310.27271460.18932516X-RAY DIFFRACTION100
2.31-2.390.25041620.18982479X-RAY DIFFRACTION100
2.39-2.490.26081300.19582510X-RAY DIFFRACTION100
2.49-2.60.22641330.19022511X-RAY DIFFRACTION100
2.6-2.740.24421250.19172544X-RAY DIFFRACTION100
2.74-2.910.24221150.18542524X-RAY DIFFRACTION100
2.91-3.130.23181560.18392514X-RAY DIFFRACTION100
3.13-3.450.20121500.17752499X-RAY DIFFRACTION100
3.45-3.950.19691160.15632567X-RAY DIFFRACTION100
3.95-4.970.17461310.14092556X-RAY DIFFRACTION100
4.97-35.80.18791330.17392590X-RAY DIFFRACTION100

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