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- PDB-3nit: The structure of UBR box (native1) -

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Basic information

Entry
Database: PDB / ID: 3nit
TitleThe structure of UBR box (native1)
ComponentsE3 ubiquitin-protein ligase UBR1
KeywordsMETAL BINDING PROTEIN / E3 ubiquitin ligase / UBR box / Zinc-binding protein / N-end rule / Ligase
Function / homology
Function and homology information


regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / proteasome regulatory particle binding / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process ...regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / proteasome regulatory particle binding / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process / protein monoubiquitination / ubiquitin ligase complex / : / 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 / 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 / MAD / Resolution: 2.6 Å
AuthorsChoi, W.S. / Jeong, B.-C. / Lee, M.-R. / Song, H.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases
Authors: Choi, W.S. / Jeong, B.-C. / Joo, Y.J. / Lee, M.-R. / Kim, J. / Eck, M.J. / Song, H.K.
History
DepositionJun 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)10,3204
Polymers10,1231
Non-polymers1963
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.207, 39.207, 274.689
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 10123.324 Da / Num. of mol.: 1 / Fragment: UBR-type domain, residues 107-194
Source method: isolated from a genetically manipulated source
Details: UBR box
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P19812
#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 / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.14 % / Mosaicity: 0.354 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M HEPES pH 7.7, 70%(v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12713,1.28305,1.28325
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Oct 1, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.127131
21.283051
31.283251
ReflectionRedundancy: 37.7 % / Av σ(I) over netI: 38.54 / Number: 129124 / Rmerge(I) obs: 0.083 / Χ2: 1.8 / D res high: 2.88 Å / D res low: 50 Å / Num. obs: 3424 / % possible obs: 97.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.25096.410.0593.71330.3
4.926.210010.072.80837.2
4.34.9210010.0632.29738.4
3.914.310010.081.85839.5
3.633.9110010.091.58440
3.413.6310010.131.30642
3.243.4110010.1751.19741.1
3.13.2410010.251.07241
2.983.199.410.3340.96838.1
2.882.9875.210.4740.80529.3
ReflectionResolution: 2.52→50 Å / Num. obs: 4701 / % possible obs: 94.2 % / Redundancy: 17.3 % / Rmerge(I) obs: 0.091 / Χ2: 1.404 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.52-2.616.40.7112640.7454.2
2.61-2.719.10.654040.93389.6
2.71-2.8413.10.5734810.84699.2
2.84-2.9919.20.514660.843100
2.99-3.1720.80.2814670.926100
3.17-3.4220.90.1844921.029100
3.42-3.76210.1124921.228100
3.76-4.3120.10.0765111.501100
4.31-5.4319.40.0645182.067100
5.43-5016.20.0586062.82497.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→31.84 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.891 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.065 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2841 199 4.5 %RANDOM
Rwork0.2439 ---
obs0.2457 4194 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.58 Å2 / Biso mean: 68.843 Å2 / Biso min: 32.95 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å21.34 Å20 Å2
2--2.68 Å20 Å2
3----4.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms690 0 3 21 714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021707
X-RAY DIFFRACTIONr_angle_refined_deg0.9341.916954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.131588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85524.32437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93415116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.315154
X-RAY DIFFRACTIONr_chiral_restr0.0630.299
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02555
X-RAY DIFFRACTIONr_nbd_refined0.1870.2255
X-RAY DIFFRACTIONr_nbtor_refined0.2870.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.29
X-RAY DIFFRACTIONr_mcbond_it0.4761.5454
X-RAY DIFFRACTIONr_mcangle_it0.8592709
X-RAY DIFFRACTIONr_scbond_it0.7783280
X-RAY DIFFRACTIONr_scangle_it1.3314.5245
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 7 -
Rwork0.466 245 -
all-252 -
obs--84.85 %
Refinement TLS params.Method: refined / Origin x: -5.159 Å / Origin y: -3.5341 Å / Origin z: -10.619 Å
111213212223313233
T0.1308 Å20.0444 Å20.0429 Å2--0.0209 Å20.0076 Å2--0.058 Å2
L3.4652 °2-0.178 °20.9799 °2-0.0556 °20.1843 °2--1.4623 °2
S0.0119 Å °0.1909 Å °0.1028 Å °0.0276 Å °-0.0327 Å °0.0192 Å °-0.091 Å °0.0101 Å °0.0208 Å °

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