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- PDB-3nim: The structure of UBR box (RRAA) -

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Basic information

Entry
Database: PDB / ID: 3nim
TitleThe structure of UBR box (RRAA)
Components
  • E3 ubiquitin-protein ligase UBR1
  • Peptide RRAA
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 / 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 / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule 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 / cellular response to unfolded protein / ubiquitin ligase complex / 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
Cysteine Rich Protein - #30 / 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 ...Cysteine Rich Protein - #30 / 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 / Cysteine Rich Protein / Ribbon / Mainly Beta
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: 2 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 1.3Nov 1, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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
B: E3 ubiquitin-protein ligase UBR1
D: E3 ubiquitin-protein ligase UBR1
F: E3 ubiquitin-protein ligase UBR1
X: Peptide RRAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,20517
Polymers37,4205
Non-polymers78512
Water4,594255
1
A: E3 ubiquitin-protein ligase UBR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4334
Polymers9,2361
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase UBR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4334
Polymers9,2361
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: E3 ubiquitin-protein ligase UBR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4334
Polymers9,2361
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: E3 ubiquitin-protein ligase UBR1
X: Peptide RRAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9075
Polymers9,7112
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.868, 44.868, 140.136
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 9236.394 Da / Num. of mol.: 4 / Fragment: UBR-type domain, residues 115-194
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: Protein/peptide Peptide RRAA


Mass: 474.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.04M sodium cacodylate trihydrate pH 6.0, 0.04M magnesium acetate tetrahydrate, 30%(v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 20, 2009
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19874 / % possible obs: 92.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Χ2: 2.289 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.075.10.59619301.53391.3
2.07-2.155.10.47519701.69691.3
2.15-2.255.10.34219971.77192.2
2.25-2.3750.28219641.89392.2
2.37-2.524.90.22919871.84592.6
2.52-2.714.80.16619542.02293.1
2.71-2.994.70.11520102.37892.2
2.99-3.424.70.07219842.87293.2
3.42-4.314.50.05319753.37493
4.31-504.90.04821033.63597

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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
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NIS

3nis


Resolution: 2→22.73 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.296 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1039 5.2 %RANDOM
Rwork0.1906 ---
obs0.1932 19825 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.09 Å2 / Biso mean: 39.8407 Å2 / Biso min: 23.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→22.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 12 255 2838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212634
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.913555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6475324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50224.203138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18515429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5071514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022070
X-RAY DIFFRACTIONr_nbd_refined0.2070.21183
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21734
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2244
X-RAY DIFFRACTIONr_metal_ion_refined0.0280.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.218
X-RAY DIFFRACTIONr_mcbond_it0.8431.51687
X-RAY DIFFRACTIONr_mcangle_it1.45322627
X-RAY DIFFRACTIONr_scbond_it1.59131059
X-RAY DIFFRACTIONr_scangle_it2.534.5928
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 76 -
Rwork0.245 1338 -
all-1414 -
obs--88.87 %

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