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- PDB-8j9r: Crystal structure of UBR box of YIFS-UBR4 -

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Basic information

Entry
Database: PDB / ID: 8j9r
TitleCrystal structure of UBR box of YIFS-UBR4
ComponentsE3 ubiquitin-protein ligase UBR4
KeywordsLIGASE / E3 ligase / UBR box
Function / homology
Function and homology information


negative regulation of HRI-mediated signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / protein K27-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization / cytoplasm protein quality control / protein K11-linked ubiquitination / tertiary granule membrane ...negative regulation of HRI-mediated signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / protein K27-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization / cytoplasm protein quality control / protein K11-linked ubiquitination / tertiary granule membrane / ficolin-1-rich granule membrane / protein K48-linked ubiquitination / specific granule membrane / positive regulation of autophagy / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / response to oxidative stress / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / calmodulin binding / endosome / protein stabilization / Neutrophil degranulation / centrosome / zinc ion binding / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / UBR4 E3 catalytic module profile. / Putative zinc finger in N-recognin (UBR box) ...E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / UBR4 E3 catalytic module profile. / 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 / Armadillo-type fold / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJeong, D.-E. / Kim, S.-J. / Shin, H.-C.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
Other governmentCRC22021-700 Korea, Republic Of
Other governmentKGM9952314 Korea, Republic Of
Other government2021M3A9G8025599 Korea, Republic Of
Citation
Journal: Commun Biol / Year: 2023
Title: Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates.
Authors: Jeong, D.E. / Lee, H.S. / Ku, B. / Kim, C.H. / Kim, S.J. / Shin, H.C.
#1: Journal: To Be Published
Title: Crystal structure of UBR box of UBR4 with YIFS
Authors: Jeong, D.-E. / Shin, H.-C.
History
DepositionMay 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UBR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6194
Polymers8,4231
Non-polymers1963
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.580, 38.280, 55.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein E3 ubiquitin-protein ligase UBR4 / 600 kDa retinoblastoma protein-associated factor / N-recognin-4 / RING-type E3 ubiquitin ...600 kDa retinoblastoma protein-associated factor / N-recognin-4 / RING-type E3 ubiquitin transferase UBR4 / Retinoblastoma-associated factor of 600 kDa / RBAF600 / p600 / Zinc finger UBR1-type protein 1


Mass: 8422.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBR4, KIAA0462, KIAA1307, RBAF600, ZUBR1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5T4S7, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris (pH5.6), 29% (w/v) polyethylene glycol 3350 (PEG3350), 0.2 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.282 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.65→27.7 Å / Num. obs: 9760 / % possible obs: 99.32 % / Redundancy: 12.3 % / Biso Wilson estimate: 13.15 Å2 / CC1/2: 0.998 / Net I/σ(I): 24.84
Reflection shellResolution: 1.65→1.709 Å / Num. unique obs: 943 / CC1/2: 0.976

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.65→27.7 Å / SU ML: 0.1794 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.1244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2871 489 5.01 %
Rwork0.2342 9273 -
obs0.2368 9760 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.04 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 3 102 672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082611
X-RAY DIFFRACTIONf_angle_d0.9943827
X-RAY DIFFRACTIONf_chiral_restr0.053987
X-RAY DIFFRACTIONf_plane_restr0.0054104
X-RAY DIFFRACTIONf_dihedral_angle_d7.640981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.890.27131590.22913008X-RAY DIFFRACTION98.66
1.89-2.380.30651600.25353049X-RAY DIFFRACTION99.38
2.38-27.70.28221700.22633216X-RAY DIFFRACTION99.97

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