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- PDB-9dno: Structure of UBR1-RFF complex -

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Basic information

Entry
Database: PDB / ID: 9dno
TitleStructure of UBR1-RFF complex
Components
  • ARG-PHE-PHE-NH2
  • E3 ubiquitin-protein ligase UBR1
KeywordsPROTEIN BINDING / UBR / E3 ligase / natural ligands
Function / homology
Function and homology information


L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cellular response to L-leucine / negative regulation of TOR signaling / ubiquitin ligase complex / proteasome complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process ...L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cellular response to L-leucine / negative regulation of TOR signaling / ubiquitin ligase complex / proteasome complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / zinc ion binding / 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 UBR1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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 CA265410 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA212119 United States
CitationJournal: To Be Published
Title: Structural Flexibility and Selectivity of N-End Rule Ligases
Authors: Huang, S.T. / 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 UBR1
B: E3 ubiquitin-protein ligase UBR1
D: ARG-PHE-PHE-NH2
E: ARG-PHE-PHE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,22710
Polymers17,8344
Non-polymers3926
Water2,810156
1
A: E3 ubiquitin-protein ligase UBR1
D: ARG-PHE-PHE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1135
Polymers8,9172
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-7 kcal/mol
Surface area4700 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UBR1
E: ARG-PHE-PHE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1135
Polymers8,9172
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-1 kcal/mol
Surface area4430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.507, 48.952, 49.946
Angle α, β, γ (deg.)90.00, 106.85, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein E3 ubiquitin-protein ligase UBR1 / N-recognin-1 / Ubiquitin-protein ligase E3-alpha-1 / Ubiquitin-protein ligase E3-alpha-I


Mass: 8449.517 Da / Num. of mol.: 2 / Fragment: UBR-box domain (UNP residues 97-168)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBR1 / Plasmid: pGEX-6p-1-hUBR1-UBRbox
Details (production host): Amp resistance, N-terminal GST tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IWV7
#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.: 156 / 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: 2.08 Å3/Da / Density % sol: 36.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: The stock concentration of UBR1UBR for co-crystallization is 7.52 mg/ml. The ligand to protein molar ratio for UBR1UBR-RFF co-crystal is 1:2, and the reservoir contains 0.1 M Bis-Tris pH 5.5 ...Details: The stock concentration of UBR1UBR for co-crystallization is 7.52 mg/ml. The ligand to protein molar ratio for UBR1UBR-RFF co-crystal is 1:2, and the reservoir contains 0.1 M Bis-Tris pH 5.5 with 24% PEG 3350. Crystals were soaked in cryoprotection liquid consisting of mother reservoir condition supplemented with 15% glycerol prior to flash freezing in liquid nitrogen.

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.23→48.97 Å / Num. obs: 36357 / % possible obs: 91.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 15.59 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10
Reflection shellResolution: 1.23→1.25 Å / Mean I/σ(I) obs: 0.1 / Num. unique obs: 909 / CC1/2: 0.053 / % possible all: 45.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→47.8 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 1452 4.92 %
Rwork0.1982 --
obs0.1987 29501 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.33→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 0 156 1360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071252
X-RAY DIFFRACTIONf_angle_d0.9711692
X-RAY DIFFRACTIONf_dihedral_angle_d6.723170
X-RAY DIFFRACTIONf_chiral_restr0.086172
X-RAY DIFFRACTIONf_plane_restr0.007226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.380.4777850.46591969X-RAY DIFFRACTION67
1.38-1.440.30521370.32362631X-RAY DIFFRACTION89
1.44-1.50.29511140.27962901X-RAY DIFFRACTION97
1.5-1.580.311590.25452892X-RAY DIFFRACTION99
1.58-1.680.21821720.21912867X-RAY DIFFRACTION97
1.68-1.810.23231610.20172937X-RAY DIFFRACTION100
1.81-1.990.22651370.20392973X-RAY DIFFRACTION100
1.99-2.280.19641760.18942910X-RAY DIFFRACTION99
2.28-2.870.19641470.18992968X-RAY DIFFRACTION100
2.87-47.80.17331640.16443001X-RAY DIFFRACTION99

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