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- PDB-3nik: The structure of UBR box (REAA) -

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Basic information

Entry
Database: PDB / ID: 3nik
TitleThe structure of UBR box (REAA)
Components
  • E3 ubiquitin-protein ligase UBR1
  • Peptide REAA
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 / cellular response to unfolded protein / protein monoubiquitination / 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: 1.85 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 REAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,17717
Polymers37,3925
Non-polymers78512
Water8,395466
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
X: Peptide REAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8795
Polymers9,6832
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: 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
Unit cell
Length a, b, c (Å)44.534, 44.534, 139.636
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 REAA


Mass: 446.478 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.: 466 / 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: 2.14 Å3/Da / Density % sol: 42.47 % / Mosaicity: 0.458 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Bis-Tris pH 6.5, 10%(w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 26430 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.078 / Χ2: 1.491 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.886.90.47313100.652100
1.88-1.926.90.42213060.705100
1.92-1.956.90.34913160.72100
1.95-1.996.90.30413170.791100
1.99-2.0470.26513520.812100
2.04-2.086.90.22612920.976100
2.08-2.146.90.19213311.05100
2.14-2.1970.1713291.006100
2.19-2.2670.15113271.072100
2.26-2.3370.13213371.139100
2.33-2.4170.12412951.207100
2.41-2.5170.11513211.322100
2.51-2.6370.11213451.531100
2.63-2.7670.10413281.882100
2.76-2.946.90.09912982.232100
2.94-3.166.90.08613242.576100
3.16-3.486.90.06713272.55799.9
3.48-3.996.60.05613182.54299.8
3.99-5.027.10.0513212.622100
5.02-506.90.04513362.4599.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
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: 1.85→38.57 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.731 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 1338 5.1 %RANDOM
Rwork0.1909 ---
obs0.1935 26383 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 306.08 Å2 / Biso mean: 31.4676 Å2 / Biso min: 15.96 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: 1.85→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 12 466 3051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212636
X-RAY DIFFRACTIONr_angle_refined_deg1.0841.913558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5615325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11424.348138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88915428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3981513
X-RAY DIFFRACTIONr_chiral_restr0.0750.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212073
X-RAY DIFFRACTIONr_mcbond_it0.6751.51635
X-RAY DIFFRACTIONr_mcangle_it1.27522632
X-RAY DIFFRACTIONr_scbond_it1.61231001
X-RAY DIFFRACTIONr_scangle_it2.5854.5926
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 108 -
Rwork0.258 1796 -
all-1904 -
obs--100 %

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