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- PDB-9dnq: Structure of UBR2-RYF complex -

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Basic information

Entry
Database: PDB / ID: 9dnq
TitleStructure of UBR2-RYF complex
Components
  • ARG-TYR-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 / male meiosis I / reciprocal meiotic recombination / negative regulation of TOR signaling / positive regulation of T cell receptor signaling pathway ...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 / male meiosis I / reciprocal meiotic recombination / negative regulation of TOR signaling / positive regulation of T cell receptor signaling pathway / protein K63-linked ubiquitination / ubiquitin ligase complex / RING-type E3 ubiquitin transferase / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / heterochromatin formation / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin / zinc ion binding / nucleus / cytosol / cytoplasm
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 / Putative zinc finger in N-recognin (UBR box) / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS ...: / 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 / Putative zinc finger in N-recognin (UBR box) / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / 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-TYR-PHE-NH2
B: E3 ubiquitin-protein ligase UBR2
D: ARG-TYR-PHE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,83410
Polymers17,4424
Non-polymers3926
Water4,396244
1
A: E3 ubiquitin-protein ligase UBR2
C: ARG-TYR-PHE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9175
Polymers8,7212
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-2 kcal/mol
Surface area4590 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UBR2
D: ARG-TYR-PHE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9175
Polymers8,7212
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-2 kcal/mol
Surface area4580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.187, 50.871, 45.956
Angle α, β, γ (deg.)90.00, 89.98, 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: 8237.357 Da / Num. of mol.: 2 / Fragment: UBR-box domain (UNP residues 98-168)
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-TYR-PHE-NH2


Mass: 483.564 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.69 Å3/Da / Density % sol: 27.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: The stock concentration of UBR2UBR for co-crystallization is 6.2 mg/ml. For UBR2UBR-RYF the ligand to protein molar ratio is 1:2 and the reservoirs contain 0.1 M Bis-Tris pH 6.3 with 26% PEG 3350.

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / 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: 33994 / % possible obs: 98.1 % / Redundancy: 4.2 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.046 / Rrim(I) all: 0.098 / Χ2: 1.723 / Net I/σ(I): 16 / Num. measured all: 141414
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.22-1.243.50.17815850.9470.9860.1050.2081.71492.4
1.24-1.263.90.18217240.9540.9880.1030.2091.65899
1.26-1.2940.18616860.9530.9880.1050.2141.6999.5
1.29-1.3140.18617340.9580.9890.1030.2131.75799.5
1.31-1.344.10.19917140.9480.9870.1070.2261.72299.5
1.34-1.374.10.19517040.9560.9890.1050.2231.70699.4
1.37-1.414.10.17717160.9660.9910.0960.2021.67799
1.41-1.453.90.17916320.9550.9880.0970.2051.70996
1.45-1.4940.16416820.9650.9910.0880.1871.64594.1
1.49-1.544.50.16216750.9740.9930.0840.1831.73399.4
1.54-1.594.30.15217570.970.9920.0790.1721.78899.7
1.59-1.664.30.14216910.9740.9930.0750.1611.68699.6
1.66-1.734.30.13217190.9790.9950.0690.151.77999.7
1.73-1.824.40.12217220.9810.9950.0640.1381.65298.6
1.82-1.9440.10716950.9810.9950.0580.1231.74597.3
1.94-2.094.10.09416340.9880.9970.050.1071.65494.2
2.09-2.34.50.08717380.990.9980.0440.0971.67799.9
2.3-2.634.50.07317260.9930.9980.0380.0821.82499.7
2.63-3.314.30.05417180.9960.9990.0290.0611.90298.1
3.31-504.40.03817420.9980.9990.020.0431.71497.2

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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→45.96 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1502 1707 5.03 %
Rwork0.1393 --
obs0.1398 33965 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 6 244 1458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061238
X-RAY DIFFRACTIONf_angle_d0.9781664
X-RAY DIFFRACTIONf_dihedral_angle_d5.899174
X-RAY DIFFRACTIONf_chiral_restr0.08162
X-RAY DIFFRACTIONf_plane_restr0.012222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.260.20691460.16892655X-RAY DIFFRACTION97
1.26-1.30.18521410.16582659X-RAY DIFFRACTION99
1.3-1.340.17841510.16072738X-RAY DIFFRACTION99
1.34-1.40.17241430.15542705X-RAY DIFFRACTION99
1.4-1.460.17771320.15262590X-RAY DIFFRACTION95
1.46-1.540.14261330.14652665X-RAY DIFFRACTION98
1.54-1.630.13591240.13032763X-RAY DIFFRACTION100
1.63-1.760.14321360.12722712X-RAY DIFFRACTION99
1.76-1.940.12911540.13252699X-RAY DIFFRACTION98
1.94-2.220.15181570.13372603X-RAY DIFFRACTION97
2.22-2.790.14981440.14032743X-RAY DIFFRACTION100
2.79-45.960.13331460.12712726X-RAY DIFFRACTION97

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