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- PDB-3nis: The structure of UBR box (native2) -

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Basic information

Entry
Database: PDB / ID: 3nis
TitleThe structure of UBR box (native2)
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
Cysteine Rich Protein - #30 / 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 / Cysteine Rich Protein / Ribbon / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / E3 ubiquitin-protein ligase UBR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,90819
Polymers36,9464
Non-polymers96215
Water4,720262
1
A: E3 ubiquitin-protein ligase UBR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4925
Polymers9,2361
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase UBR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4925
Polymers9,2361
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
MethodPISA
4
F: E3 ubiquitin-protein ligase UBR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4925
Polymers9,2361
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.576, 44.576, 140.055
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.17 Å3/Da / Density % sol: 43.43 % / Mosaicity: 0.475 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.02M calcium chloride dehydrate, 0.1M sodium acetate trihydrate pH 4.8, 30%(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: 1.1 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Feb 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 35555 / % possible obs: 100 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.091 / Χ2: 1.793 / Net I/σ(I): 9.9 / Num. measured all: 270967
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.68-1.746.80.52134950.76999.9
1.74-1.817.70.41635620.824100
1.81-1.897.80.33735730.855100
1.89-1.997.80.23235670.99100
1.99-2.127.90.16635561.256100
2.12-2.287.90.13135481.679100
2.28-2.517.90.1135762.047100
2.51-2.877.80.09135502.508100
2.87-3.627.50.06835463.317100
3.62-507.10.05835823.77399.7

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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
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NIT

3nit


Resolution: 1.68→25.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.638 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 1778 5 %RANDOM
Rwork0.1929 ---
obs0.1944 35466 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.03 Å2 / Biso mean: 25.003 Å2 / Biso min: 8.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.68→25.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 24 262 2828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212616
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.9123529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57324.37135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96515422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0551512
X-RAY DIFFRACTIONr_chiral_restr0.070.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022060
X-RAY DIFFRACTIONr_nbd_refined0.190.21146
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21716
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2238
X-RAY DIFFRACTIONr_metal_ion_refined0.0190.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.221
X-RAY DIFFRACTIONr_mcbond_it0.5991.51692
X-RAY DIFFRACTIONr_mcangle_it1.02522614
X-RAY DIFFRACTIONr_scbond_it1.28431041
X-RAY DIFFRACTIONr_scangle_it1.9314.5915
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 126 -
Rwork0.238 2498 -
all-2624 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1408-0.3998-0.06181.2780.48530.9523-0.06920.02840.04160.10890.1177-0.0307-0.0015-0.0522-0.04850.03320.04950.0020.02470.0136-0.0155-26.88148.6237-1.1553
21.6588-0.1567-0.13720.7855-0.71641.2250.0335-0.00760.0136-0.0626-0.0122-0.04380.1912-0.0539-0.02130.085-0.08590.03620.0225-0.04470.0023-20.63348.084722.79
32.45382.1702-0.26783.4947-0.25660.8341-0.0006-0.00850.3756-0.0738-0.06460.45190.09650.07160.06520.0366-0.0327-0.00530.03180.00250.0726-36.3174-8.540720.7054
40.8449-1.03150.48232.5951-0.09581.00850.00040.06790.11150.0710.0752-0.2067-0.00190.0496-0.07570.00160.04420.01050.0273-0.01290.0369-10.9343-8.113-2.0404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 194
2X-RAY DIFFRACTION2B113 - 194
3X-RAY DIFFRACTION3D113 - 193
4X-RAY DIFFRACTION4F113 - 194

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