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- PDB-6kgi: RLGS-yUbr1 Ubr box -

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Basic information

Entry
Database: PDB / ID: 6kgi
TitleRLGS-yUbr1 Ubr box
ComponentsE3 ubiquitin-protein ligase UBR1
KeywordsLIGASE / Ubr1 / Ubr box
Function / homology
Function and homology information


regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / proteasome regulatory particle binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / stress-induced homeostatically regulated protein degradation pathway / mitochondria-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation ...regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / proteasome regulatory particle binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / stress-induced homeostatically regulated protein degradation pathway / mitochondria-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein monoubiquitination / ubiquitin ligase complex / cellular response to unfolded protein / ERAD pathway / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding / cytoplasm
Similarity search - Function
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 / 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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsHeo, J. / Kwon, D.H. / Kim, L. / Song, H.K.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway.
Authors: Kim, L. / Kwon, D.H. / Heo, J. / Park, M.R. / Song, H.K.
History
DepositionJul 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase UBR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8754
Polymers9,6791
Non-polymers1963
Water57632
1
B: E3 ubiquitin-protein ligase UBR1
hetero molecules

B: E3 ubiquitin-protein ligase UBR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7508
Polymers19,3582
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1380 Å2
ΔGint-13 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.630, 60.630, 69.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein E3 ubiquitin-protein ligase UBR1 / N-end-recognizing protein / N-recognin-1 / RING-type E3 ubiquitin transferase UBR1


Mass: 9678.886 Da / Num. of mol.: 1 / Fragment: Ubr box
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UBR1, PTR1, YGR184C, G7168 / Production host: Escherichia coli (E. coli)
References: UniProt: P19812, 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-Tris pH 6.5, 2.7-3.0M NaCl

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 62982 / % possible obs: 100 % / Redundancy: 12.5 % / Net I/σ(I): 43.9
Reflection shellResolution: 1.04→1.06 Å / Num. unique obs: 6200

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NIT

3nit


Resolution: 1.04→30.25 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.89
RfactorNum. reflection% reflection
Rfree0.2018 2000 3.17 %
Rwork0.1894 61019 -
obs0.1898 62982 100 %
Solvent computationShrinkage radii: 0.99 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.8948 Å2
Refinement stepCycle: LAST / Resolution: 1.04→30.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms669 0 3 32 704
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.0398-1.06580.23891400.24842994439
1.0658-1.09470.24481410.219642894430
1.0947-1.12690.20051420.19843054447
1.1269-1.16330.18791400.184842934433
1.1633-1.20480.18011410.181542864427
1.2048-1.25310.181410.179643094450
1.2531-1.31010.20011420.175643224464
1.3101-1.37920.19031420.173343494491
1.3792-1.46560.18681420.172843214463
1.4656-1.57870.15471420.163443434485
1.5787-1.73760.15631430.160243814524
1.7376-1.9890.16961450.17743924537
1.989-2.50570.20171460.19444624608
2.5057-30.32790.24291530.20846684821

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