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- PDB-9dnp: Structure of UBR2-RFF complex -

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Basic information

Entry
Database: PDB / ID: 9dnp
TitleStructure of UBR2-RFF complex
Components
  • ARG-PHE-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-PHE-PHE-NH2
B: E3 ubiquitin-protein ligase UBR2
D: ARG-PHE-PHE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,49410
Polymers17,1024
Non-polymers3926
Water4,053225
1
A: E3 ubiquitin-protein ligase UBR2
C: ARG-PHE-PHE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7475
Polymers8,5512
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-2 kcal/mol
Surface area4290 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UBR2
D: ARG-PHE-PHE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7475
Polymers8,5512
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-2 kcal/mol
Surface area4480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.538, 56.987, 115.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-399-

HOH

21B-377-

HOH

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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: 8083.191 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-hUBR1-UBRbox
Details (production host): Amp resistance, N-terminal GST tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IWV8
#2: Protein/peptide ARG-PHE-PHE-NH2


Mass: 467.564 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.: 225 / 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: 2.32 Å3/Da / Density % sol: 47 %
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-RFF 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: 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: 47384 / % possible obs: 95.3 % / Redundancy: 6.8 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.038 / Rrim(I) all: 0.104 / Χ2: 1.29 / Net I/σ(I): 7.2 / Num. measured all: 320088
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.22-1.242.31.28112940.1950.5710.8661.5630.50153.2
1.24-1.262.81.19318320.320.6960.7511.4240.48573.3
1.26-1.293.91.25821630.3830.7450.6791.4390.47589.1
1.29-1.315.11.04723410.4590.7930.4911.1630.50395
1.31-1.346.10.98923890.6160.8730.4211.0790.50297.7
1.34-1.376.90.82424510.7270.9180.3330.8910.55299.5
1.37-1.417.20.67624840.7940.9410.2660.7280.62399.7
1.41-1.456.60.59724340.8360.9540.2450.6470.65499.8
1.45-1.497.10.44624520.8820.9680.1760.4810.7699.8
1.49-1.548.10.38924700.9280.9810.1450.4160.909100
1.54-1.597.90.32124780.9420.9850.1210.3431.226100
1.59-1.667.90.2624780.9610.990.0980.2781.557100
1.66-1.737.60.21724640.9770.9940.0830.2321.78899.9
1.73-1.827.50.17824790.9830.9960.0690.1911.8599.8
1.82-1.946.70.17224700.9820.9950.0710.1861.95299.9
1.94-2.096.60.11324960.9930.9980.0460.1221.81499.7
2.09-2.380.12424980.9910.9980.0460.1321.847100
2.3-2.638.10.09925200.9930.9980.0360.1051.83999.8
2.63-3.317.70.08125430.9950.9990.030.0871.64199.8
3.31-507.20.05326480.9980.9990.020.0571.77399.2

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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→37.81 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 2381 5.09 %
Rwork0.1863 --
obs0.1871 46805 94.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 6 225 1407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061204
X-RAY DIFFRACTIONf_angle_d0.9021615
X-RAY DIFFRACTIONf_dihedral_angle_d6.458167
X-RAY DIFFRACTIONf_chiral_restr0.071158
X-RAY DIFFRACTIONf_plane_restr0.009215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.3438550.33951242X-RAY DIFFRACTION45
1.25-1.270.34851200.33861965X-RAY DIFFRACTION72
1.27-1.30.31731270.31432490X-RAY DIFFRACTION91
1.3-1.340.29431460.29182611X-RAY DIFFRACTION96
1.34-1.370.26371430.26362735X-RAY DIFFRACTION99
1.37-1.410.26761470.25192765X-RAY DIFFRACTION100
1.41-1.460.24831450.24452710X-RAY DIFFRACTION99
1.46-1.510.21681270.21382759X-RAY DIFFRACTION100
1.51-1.570.20251600.19152751X-RAY DIFFRACTION100
1.57-1.640.18421340.18682785X-RAY DIFFRACTION100
1.64-1.730.17561440.18032775X-RAY DIFFRACTION100
1.73-1.840.20631540.18332744X-RAY DIFFRACTION100
1.84-1.980.22041460.20142761X-RAY DIFFRACTION99
1.98-2.180.19741590.18072781X-RAY DIFFRACTION100
2.18-2.490.19511550.18472792X-RAY DIFFRACTION100
2.49-3.140.2081610.17672843X-RAY DIFFRACTION100
3.14-37.810.17241580.15572915X-RAY DIFFRACTION99

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