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- PDB-9v0k: UBR box of human UBR1 -

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Basic information

Entry
Database: PDB / ID: 9v0k
TitleUBR box of human UBR1
ComponentsE3 ubiquitin-protein ligase UBR1
KeywordsLIGASE
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
: / PHOSPHATE ION / E3 ubiquitin-protein ligase UBR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsLee, S. / Song, H.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of human UBR1 UBR box
Authors: Lee, S.H. / Song, H.K.
History
DepositionMay 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,77512
Polymers16,1702
Non-polymers60510
Water2,378132
1
A: E3 ubiquitin-protein ligase UBR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4156
Polymers8,0851
Non-polymers3305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-5 kcal/mol
Surface area4470 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UBR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3606
Polymers8,0851
Non-polymers2745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.147, 30.165, 63.154
Angle α, β, γ (deg.)90.000, 113.700, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,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: 8085.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBR1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IWV7, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion
Details: Sodium phosphate monobasic monohydrate, potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→29.1 Å / Num. obs: 38619 / % possible obs: 97.67 % / Redundancy: 6 % / Biso Wilson estimate: 5.95 Å2 / Rmerge(I) obs: 0.1533 / Net I/σ(I): 10.92
Reflection shellResolution: 1.54→1.595 Å / Num. unique obs: 1958 / CC1/2: 0.652

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
HKL-2000720data scaling
PHENIX1.20.1-4487phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→29.1 Å / SU ML: 0.1476 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.9511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2065 3787 9.81 %
Rwork0.1711 34832 -
obs0.1745 38619 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.39 Å2
Refinement stepCycle: LAST / Resolution: 1.54→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 14 132 1260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881153
X-RAY DIFFRACTIONf_angle_d1.0591553
X-RAY DIFFRACTIONf_chiral_restr0.0526159
X-RAY DIFFRACTIONf_plane_restr0.0118204
X-RAY DIFFRACTIONf_dihedral_angle_d6.759157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.33951200.29881103X-RAY DIFFRACTION82.36
1.56-1.580.29921360.27191267X-RAY DIFFRACTION93.16
1.58-1.60.30461380.25151210X-RAY DIFFRACTION93.55
1.6-1.620.24331350.25471256X-RAY DIFFRACTION93.54
1.62-1.650.281410.24241290X-RAY DIFFRACTION94.33
1.65-1.670.26611400.22791301X-RAY DIFFRACTION94.8
1.67-1.70.22511340.20981231X-RAY DIFFRACTION94.4
1.7-1.730.24721350.19961273X-RAY DIFFRACTION94.56
1.73-1.760.22471390.19571270X-RAY DIFFRACTION94.82
1.76-1.790.17861370.18821271X-RAY DIFFRACTION95.01
1.79-1.830.22641390.17861282X-RAY DIFFRACTION94.86
1.83-1.870.21671370.17711307X-RAY DIFFRACTION95.88
1.87-1.910.22981330.17061272X-RAY DIFFRACTION96.43
1.91-1.960.20561460.16741310X-RAY DIFFRACTION97.26
1.96-2.020.20241450.15961330X-RAY DIFFRACTION97.49
2.02-2.080.18171420.15811284X-RAY DIFFRACTION97.81
2.08-2.140.16811450.14041359X-RAY DIFFRACTION98.3
2.14-2.220.18011440.14071282X-RAY DIFFRACTION98.48
2.22-2.310.21841500.13451342X-RAY DIFFRACTION99
2.31-2.410.18911450.14341324X-RAY DIFFRACTION99.12
2.41-2.540.20011440.15241337X-RAY DIFFRACTION99.33
2.54-2.70.22451440.15651342X-RAY DIFFRACTION99.33
2.7-2.910.1851400.15181317X-RAY DIFFRACTION99.05
2.91-3.20.1661460.1591306X-RAY DIFFRACTION96.86
3.2-3.660.20651450.14631314X-RAY DIFFRACTION98.12
3.66-4.610.13951390.1361334X-RAY DIFFRACTION98.66
4.61-29.10.20881480.17351318X-RAY DIFFRACTION97.6

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