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- PDB-9mux: Structure of UBR1-RWA complex -

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Basic information

Entry
Database: PDB / ID: 9mux
TitleStructure of UBR1-RWA complex
Components
  • ARG-TRP-ALA-NH2 peptide
  • E3 ubiquitin-protein ligase UBR1
KeywordsLIGASE / UBR / E3 ligase / natural ligands / PROTEIN BINDING
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: 1.29 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)RO1 CA212119 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)RO1 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. / Chen, D. / Ren, T. / Thomas, N. / Sankaran, B. / Jones, R.
History
DepositionJan 14, 2025Deposition 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
D: ARG-TRP-ALA-NH2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0765
Polymers8,8802
Non-polymers1963
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Single peal observed during size exclusion chromatography purification
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-1 kcal/mol
Surface area5010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.091, 43.809, 27.085
Angle α, β, γ (deg.)90.00, 111.27, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 1 / 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, RING-type E3 ubiquitin transferase
#2: Protein/peptide ARG-TRP-ALA-NH2 peptide


Mass: 430.504 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.: 81 / 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: 1.8 Å3/Da / Density % sol: 31.68 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES buffer 25%PEG3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 14074 / % possible obs: 94.24 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.021 / Rsym value: 0.042 / Χ2: 0.986 / Net I/σ(I): 19.471
Reflection shellResolution: 1.29→1.31 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 19.471 / Num. unique obs: 298 / CC1/2: 0.986 / Rpim(I) all: 0.056 / % possible all: 82.4

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
DIALSdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→25.25 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 15.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1507 634 4.51 %
Rwork0.1417 --
obs0.1421 14057 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.29→25.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms618 0 0 81 699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007646
X-RAY DIFFRACTIONf_angle_d0.928876
X-RAY DIFFRACTIONf_dihedral_angle_d13.421229
X-RAY DIFFRACTIONf_chiral_restr0.07689
X-RAY DIFFRACTIONf_plane_restr0.008117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.390.1931240.16092412X-RAY DIFFRACTION86
1.39-1.530.14351310.14542659X-RAY DIFFRACTION94
1.53-1.750.15311210.12722718X-RAY DIFFRACTION96
1.75-2.20.14841260.14442772X-RAY DIFFRACTION97
2.21-25.250.14391320.14112862X-RAY DIFFRACTION98

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