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- PDB-4kbl: Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibit... -

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Basic information

Entry
Database: PDB / ID: 4kbl
TitleStructure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism
ComponentsE3 ubiquitin-protein ligase ARIH1
KeywordsLIGASE / RING-IBR-RING / E3 ubiquitin ligase
Function / homology
Function and homology information


PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / Lewy body / RBR-type E3 ubiquitin transferase / ubiquitin conjugating enzyme binding / Cajal body / ubiquitin ligase complex / PKR-mediated signaling / ISG15 antiviral mechanism / protein polyubiquitination ...PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / Lewy body / RBR-type E3 ubiquitin transferase / ubiquitin conjugating enzyme binding / Cajal body / ubiquitin ligase complex / PKR-mediated signaling / ISG15 antiviral mechanism / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / nuclear body / protein ubiquitination / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1750 / : / E3 ubiquitin-protein ligase ARIH1, UBA-like domain / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1750 / : / E3 ubiquitin-protein ligase ARIH1, UBA-like domain / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ring finger / Four Helix Bundle (Hemerythrin (Met), subunit A) / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ARIH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsDuda, D.M. / Olszewski, J.L. / Schulman, B.A.
CitationJournal: Structure / Year: 2013
Title: Structure of HHARI, a RING-IBR-RING Ubiquitin Ligase: Autoinhibition of an Ariadne-Family E3 and Insights into Ligation Mechanism.
Authors: Duda, D.M. / Olszewski, J.L. / Schuermann, J.P. / Kurinov, I. / Miller, D.J. / Nourse, A. / Alpi, A.F. / Schulman, B.A.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Feb 28, 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_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_seq_id / _struct_conn.ptnr2_label_asym_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 ARIH1
B: E3 ubiquitin-protein ligase ARIH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,46914
Polymers128,6842
Non-polymers78512
Water0
1
A: E3 ubiquitin-protein ligase ARIH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7347
Polymers64,3421
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase ARIH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7347
Polymers64,3421
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-12 kcal/mol
Surface area42700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.403, 147.403, 86.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein E3 ubiquitin-protein ligase ARIH1 / H7-AP2 / HHARI / Monocyte protein 6 / MOP-6 / Protein ariadne-1 homolog / ARI-1 / UbcH7-binding ...H7-AP2 / HHARI / Monocyte protein 6 / MOP-6 / Protein ariadne-1 homolog / ARI-1 / UbcH7-binding protein / UbcM4-interacting protein / Ubiquitin-conjugating enzyme E2-binding protein 1


Mass: 64341.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARIH1, ARI, MOP6, UBCH7BP, HUSSY-27 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y4X5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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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: 3.66 Å3/Da / Density % sol: 78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.92M potassium / sodium tartrate, 0.2M lithium sulfate, 0.1M CHES, 5% ethylene glycol, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2012
RadiationMonochromator: Cryo-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.3→46.67 Å / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.3→3.48 Å / % possible all: 96.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(Autosol)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALAdata scaling
PHENIX(Autosol)phasing
RefinementResolution: 3.3→46.613 Å / SU ML: 1.2 / σ(F): 0 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 4034 7.82 %RANDOM
Rwork0.2313 ---
obs0.2353 51574 92.36 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 98.34 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.3→46.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6569 0 12 0 6581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086776
X-RAY DIFFRACTIONf_angle_d1.3939141
X-RAY DIFFRACTIONf_dihedral_angle_d20.4052514
X-RAY DIFFRACTIONf_chiral_restr0.108942
X-RAY DIFFRACTIONf_plane_restr0.0051152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2825-3.32110.37841030.35511300X-RAY DIFFRACTION72
3.3211-3.36160.39371470.35821605X-RAY DIFFRACTION90
3.3616-3.40410.40541270.36011471X-RAY DIFFRACTION86
3.4041-3.44890.34351180.33971430X-RAY DIFFRACTION79
3.4489-3.49610.3041260.32621572X-RAY DIFFRACTION87
3.4961-3.54610.35171490.31891698X-RAY DIFFRACTION97
3.5461-3.5990.33141350.31391692X-RAY DIFFRACTION96
3.599-3.65520.28371510.31061718X-RAY DIFFRACTION96
3.6552-3.71510.3381530.2691700X-RAY DIFFRACTION97
3.7151-3.77910.31451440.2681719X-RAY DIFFRACTION96
3.7791-3.84780.27341460.26631654X-RAY DIFFRACTION96
3.8478-3.92180.31351550.25061748X-RAY DIFFRACTION96
3.9218-4.00180.27721390.23181682X-RAY DIFFRACTION96
4.0018-4.08880.29831490.23721690X-RAY DIFFRACTION96
4.0888-4.18380.29541430.22621695X-RAY DIFFRACTION95
4.1838-4.28840.22611480.21071690X-RAY DIFFRACTION95
4.2884-4.40420.22641370.20521660X-RAY DIFFRACTION94
4.4042-4.53370.26711260.19871470X-RAY DIFFRACTION83
4.5337-4.67990.20471340.19241592X-RAY DIFFRACTION91
4.6799-4.8470.27621450.1811748X-RAY DIFFRACTION96
4.847-5.04090.28761380.20491711X-RAY DIFFRACTION97
5.0409-5.270.32271440.21671685X-RAY DIFFRACTION96
5.27-5.54740.32631430.25041718X-RAY DIFFRACTION96
5.5474-5.89440.36791500.24341716X-RAY DIFFRACTION96
5.8944-6.34840.37591400.27851661X-RAY DIFFRACTION94
6.3484-6.98540.27861250.26941496X-RAY DIFFRACTION85
6.9854-7.99180.29291450.19141698X-RAY DIFFRACTION96
7.9918-10.05220.20221320.16741740X-RAY DIFFRACTION96
10.0522-46.61760.25331420.23431581X-RAY DIFFRACTION90
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)
13.9818-0.9629-0.96080.8990.07580.9745-0.034-0.10370.19480.25960.0835-0.22920.08210.0312-0.05171.2208-0.05340.01540.945-0.02771.079471.2196119.95957.4834
20.8687-0.7394-0.21783.55540.80281.08510.01690.19290.1326-0.21350.0381-0.07370.0389-0.0672-0.06840.7701-0.05770.01781.1361-0.05010.893745.9444145.317-8.2106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A)
2X-RAY DIFFRACTION2(chain B)

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