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- PDB-8b5w: Crystal structure of the E3 module from UBR4 -

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Basic information

Entry
Database: PDB / ID: 8b5w
TitleCrystal structure of the E3 module from UBR4
ComponentscDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA
KeywordsLIGASE / ubiquitin / E3 ligase / zinc finger
Function / homologyE3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / ligase activity / cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsVirdee, S. / Mabbitt, P.D. / Barnsby-Greer, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: UBE2A and UBE2B are recruited by an atypical E3 ligase module in UBR4.
Authors: Barnsby-Greer, L. / Mabbitt, P.D. / Dery, M.A. / Squair, D.R. / Wood, N.T. / Lamoliatte, F. / Lange, S.M. / Virdee, S.
History
DepositionSep 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: 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_DOI / _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: cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9454
Polymers51,7561
Non-polymers1903
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint5 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.131, 84.644, 148.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA


Mass: 51755.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B3KMT2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10 mM Na2HPO4 13% PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.2820 or 1.2831
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2821
21.28311
ReflectionResolution: 1.8→74.07 Å / Num. obs: 36081 / % possible obs: 91.33 % / Redundancy: 2 % / Biso Wilson estimate: 24.64 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02395 / Rpim(I) all: 0.02395 / Rrim(I) all: 0.03387 / Net I/σ(I): 23.84
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2907 / Mean I/σ(I) obs: 2.56 / Num. unique obs: 3577 / CC1/2: 0.872 / CC star: 0.965 / Rpim(I) all: 0.2907 / Rrim(I) all: 0.4111 / % possible all: 91.67

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
DIALSdata reduction
DIALSdata scaling
CRANK22.01phasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→74.07 Å / SU ML: 0.2153 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.3732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 1747 4.84 %
Rwork0.1981 34329 -
obs0.1993 36076 91.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→74.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 9 408 3140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252799
X-RAY DIFFRACTIONf_angle_d0.54323810
X-RAY DIFFRACTIONf_chiral_restr0.0401426
X-RAY DIFFRACTIONf_plane_restr0.0041490
X-RAY DIFFRACTIONf_dihedral_angle_d4.9582376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.32811410.2552790X-RAY DIFFRACTION90.83
1.85-1.90.27481210.25772624X-RAY DIFFRACTION96.55
1.93-1.980.30621350.25142464X-RAY DIFFRACTION99.96
1.98-2.040.31681250.2432451X-RAY DIFFRACTION99.81
2.09-2.150.25811140.21692113X-RAY DIFFRACTION99.91
2.15-2.270.23081440.21293119X-RAY DIFFRACTION100
2.27-2.410.22281590.20843137X-RAY DIFFRACTION100
2.41-2.60.24291780.21053086X-RAY DIFFRACTION100
2.6-2.860.24831550.20093153X-RAY DIFFRACTION100
2.86-3.270.2461420.20073165X-RAY DIFFRACTION99.97
3.27-4.120.19041460.17522933X-RAY DIFFRACTION92.41
4.12-74.070.17031870.1723294X-RAY DIFFRACTION99.91

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