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- PDB-5tdc: Crystal structure of the human UBR-box domain from UBR1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5tdc
TitleCrystal structure of the human UBR-box domain from UBR1 in complex with monomethylated arginine peptide.
Components
  • E3 ubiquitin-protein ligase UBR1
  • NMM-ILE-PHE-SER peptide
KeywordsLIGASE / UBR-box / N-end rule / N-degron / monomethylated arginine
Function / homology
Function and homology information


L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cellular response to L-leucine / negative regulation of TOR signaling / ubiquitin ligase complex / proteasome complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process ...L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cellular response to L-leucine / negative regulation of TOR signaling / ubiquitin ligase complex / proteasome complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
: / E3 ubiquitin-protein ligase ELL-like / 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 / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Putative zinc finger in N-recognin (UBR box) ...: / E3 ubiquitin-protein ligase ELL-like / 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 / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / 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 / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.607 Å
AuthorsKozlov, G. / Munoz-Escobar, J. / Matta-Camacho, E. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Structure / Year: 2017
Title: Bound Waters Mediate Binding of Diverse Substrates to a Ubiquitin Ligase.
Authors: Munoz-Escobar, J. / Matta-Camacho, E. / Cho, C. / Kozlov, G. / Gehring, K.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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
C: E3 ubiquitin-protein ligase UBR1
B: NMM-ILE-PHE-SER peptide
D: NMM-ILE-PHE-SER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,29912
Polymers17,7144
Non-polymers5858
Water1,27971
1
A: E3 ubiquitin-protein ligase UBR1
B: NMM-ILE-PHE-SER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1496
Polymers8,8572
Non-polymers2924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-28 kcal/mol
Surface area4410 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase UBR1
D: NMM-ILE-PHE-SER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1496
Polymers8,8572
Non-polymers2924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-41 kcal/mol
Surface area4730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.274, 49.036, 53.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase UBR1 / N-recognin-1 / Ubiquitin-protein ligase E3-alpha-1 / Ubiquitin-protein ligase E3-alpha-I


Mass: 8321.388 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBR1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q8IWV7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide NMM-ILE-PHE-SER peptide


Mass: 535.637 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.73 Å3/Da / Density % sol: 28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M (NH4)2SO4, 0.2 K/Na Tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9769 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 1.607→28.736 Å / Num. obs: 16360 / % possible obs: 97.39 % / Redundancy: 2.4 % / Net I/σ(I): 13.26
Reflection shellResolution: 1.607→1.63 Å / Redundancy: 1.6 % / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NY1

3ny1


Resolution: 1.607→28.736 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1804 827 5.06 %
Rwork0.1489 --
obs0.1505 16360 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.607→28.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 16 71 1238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091228
X-RAY DIFFRACTIONf_angle_d1.051626
X-RAY DIFFRACTIONf_dihedral_angle_d12.992695
X-RAY DIFFRACTIONf_chiral_restr0.062170
X-RAY DIFFRACTIONf_plane_restr0.008209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6074-1.70810.1971210.19032246X-RAY DIFFRACTION86
1.7081-1.83990.21111560.15682556X-RAY DIFFRACTION98
1.8399-2.0250.20041400.14422603X-RAY DIFFRACTION100
2.025-2.31790.1521510.13232629X-RAY DIFFRACTION100
2.3179-2.91990.17681350.14872673X-RAY DIFFRACTION100
2.9199-28.7410.17911240.14912826X-RAY DIFFRACTION100
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)
10.3080.00790.02140.2061-0.03390.05520.09410.0568-0.08-0.1235-0.0404-0.01280.00730.0686-0.00010.20990.0034-0.01610.14070.02410.13318.69634.52120.9508
20.33150.37480.08750.7346-0.2470.40040.01470.07320.04940.114-0.0135-0.0526-0.08380.0479-00.13950.0045-0.00330.14410.01990.169312.58681.979928.2981
30.4019-0.02890.25930.6906-0.07680.3977-0.005-0.016-0.10570.08960.0457-0.0365-0.19850.00180.00290.15950.0119-0.00590.11640.01160.129812.80420.705627.6283
40.04210.01170.00220.01690.03060.06350.0816-0.2902-0.2070.1389-0.0225-0.14480.4939-0.3414-0.00030.1702-0.03080.00180.18050.02830.19231.6993-5.158529.9779
50.3283-0.188-0.09530.99220.49990.2533-0.11010.20320.3157-0.07460.2446-0.2106-0.2215-0.22640.04630.16410.03360.03010.2160.01050.1421-8.89345.32439.9013
60.17290.13240.10090.1465-0.08740.63670.00650.02560.0206-0.09520.0191-0.0458-0.08610.01680.00010.1234-0.00710.00030.1332-0.00480.1361-8.97790.66422.1046
70.0362-0.0026-0.0480.1214-0.02640.0637-0.00540.1481-0.1981-0.07090.0579-0.06670.22220.0165-00.13820.02450.00810.21550.00540.131-3.0794-1.795122.8945
80.2591-0.15250.12870.36940.03830.24930.02630.0767-0.1107-0.1442-0.01660.0097-0.1466-0.0693-0.00080.10830.0154-0.00430.1656-0.01540.1283-14.6547-1.420517.1489
90.12870.05540.12880.12580.18070.28170.34560.36370.66550.0183-0.22630.0980.0482-0.35550.0060.17160.03240.0110.1988-0.00040.1963-19.98078.978721.9318
101.1203-0.5682-2.96030.44332.301920.09440.3343-0.1029-0.0826-0.1484-0.0920.02050.1430.00710.16790.05840.00040.241-0.0070.144618.0062.427715.7125
110.04810.03260.01340.07260.10070.1746-0.03740.134-0.4075-0.5032-0.21680.10790.0751-0.02650.00140.30350.02110.02070.2519-0.05620.2182-7.3365-6.85748.244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 98 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 130 )
3X-RAY DIFFRACTION3chain 'A' and (resid 131 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 167 )
5X-RAY DIFFRACTION5chain 'C' and (resid 98 through 107 )
6X-RAY DIFFRACTION6chain 'C' and (resid 108 through 135 )
7X-RAY DIFFRACTION7chain 'C' and (resid 136 through 142 )
8X-RAY DIFFRACTION8chain 'C' and (resid 143 through 162 )
9X-RAY DIFFRACTION9chain 'C' and (resid 163 through 168 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 3 )
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 4 )

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