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- PDB-9dnr: Structure of UBR2-RWF complex -

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Basic information

Entry
Database: PDB / ID: 9dnr
TitleStructure of UBR2-RWF complex
Components
  • ARG-TRP-PHE-NH2
  • E3 ubiquitin-protein ligase UBR2
KeywordsPROTEIN BINDING / UBR / E3 ligase / natural ligands
Function / homology
Function and homology information


histone H2A ubiquitin ligase activity / L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / male meiotic nuclear division / transposable element silencing / cellular response to L-leucine / negative regulation of TOR signaling / reciprocal meiotic recombination / positive regulation of T cell receptor signaling pathway / male meiosis I ...histone H2A ubiquitin ligase activity / L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / male meiotic nuclear division / transposable element silencing / cellular response to L-leucine / negative regulation of TOR signaling / reciprocal meiotic recombination / positive regulation of T cell receptor signaling pathway / male meiosis I / protein K63-linked ubiquitination / ubiquitin ligase complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / heterochromatin formation / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / : / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Putative zinc finger in N-recognin (UBR box) ...: / E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / : / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsHuang, S. / Wu, J. / Taylor, S. / Chen, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)HT9425-23-1-0560 United States
Department of Defense (DOD, United States)PA220024P1 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA212119 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA265410 United States
CitationJournal: To Be Published
Title: Structural Flexibility and Selectivity of N-End Rule Ligases
Authors: Huang, S. / Wu, J. / Taylor, S. / Chen, Y.
History
DepositionSep 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UBR2
C: ARG-TRP-PHE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5295
Polymers8,3332
Non-polymers1963
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Single peak observed during size exclusion chromatography purification
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-1 kcal/mol
Surface area4150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.235, 36.957, 29.615
Angle α, β, γ (deg.)90.00, 109.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein E3 ubiquitin-protein ligase UBR2 / N-recognin-2 / Ubiquitin-protein ligase E3-alpha-2 / Ubiquitin-protein ligase E3-alpha-II


Mass: 7825.902 Da / Num. of mol.: 1 / Fragment: UBR-box domain (UNP residues 98-167)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBR2, C6orf133, KIAA0349 / Plasmid: pGEX-6p-1-hUBR2-UBRbox
Details (production host): Amp resistance, N-terminal GST tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IWV8
#2: Protein/peptide ARG-TRP-PHE-NH2


Mass: 506.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.81 Å3/Da / Density % sol: 32.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: For UBR2UBR-RWF co-crystal, the ligand to protein molar ratio is 1:5 and the reservoir contains 0.1 M Bis-Tris pH6.3 with 29% PEG 3350. The stock concentration of UBR2UBR for co-crystallization is 6.2 mg/ml.

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 17252 / % possible obs: 96.4 % / Redundancy: 4.1 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.037 / Rrim(I) all: 0.079 / Χ2: 1.701 / Net I/σ(I): 23.2 / Num. measured all: 71322
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.22-1.243.80.1737180.9510.9870.0930.1971.84781.2
1.24-1.264.10.1758130.9750.9940.090.1981.74592.8
1.26-1.294.10.1658600.980.9950.0850.1861.67195.8
1.29-1.314.10.1618680.9770.9940.0830.1821.65396.9
1.31-1.344.20.1728550.970.9920.0870.1931.63597.9
1.34-1.374.20.1638770.9790.9950.0830.1831.73498.4
1.37-1.414.10.1578740.9790.9950.080.1771.797.7
1.41-1.453.80.1528570.9740.9930.0790.1721.74497.2
1.45-1.493.80.1338430.980.9950.070.1511.74994.3
1.49-1.544.40.1328860.9850.9960.0670.1481.67698.6
1.54-1.594.40.1258620.9810.9950.0630.141.72998.3
1.59-1.664.40.1178870.9850.9960.0590.1311.6598.7
1.66-1.734.20.1079020.9870.9970.0550.1211.71598.6
1.73-1.824.20.0968670.9880.9970.0490.1081.63698.9
1.82-1.943.90.0878630.9920.9980.0460.0991.6496.2
1.94-2.093.90.0748640.9930.9980.040.0851.71896.1
2.09-2.34.40.0698870.9950.9990.0350.0771.62599.1
2.3-2.634.40.0618920.9940.9980.0310.0681.64698.7
2.63-3.314.10.0488980.9960.9990.0260.0551.62498.4
3.31-504.10.0378790.9970.9990.020.0421.94994.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→27.91 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 17.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1799 866 5.02 %
Rwork0.1676 --
obs0.1682 17238 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→27.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms562 0 3 95 660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007574
X-RAY DIFFRACTIONf_angle_d0.955771
X-RAY DIFFRACTIONf_dihedral_angle_d6.36181
X-RAY DIFFRACTIONf_chiral_restr0.08577
X-RAY DIFFRACTIONf_plane_restr0.008103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.30.19891410.19062607X-RAY DIFFRACTION94
1.3-1.40.18881460.18212751X-RAY DIFFRACTION98
1.4-1.540.19661320.17522723X-RAY DIFFRACTION97
1.54-1.760.16111600.15332743X-RAY DIFFRACTION99
1.76-2.220.18061400.17012736X-RAY DIFFRACTION97
2.22-27.910.17751470.16192812X-RAY DIFFRACTION97

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