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- PDB-4kc9: Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibit... -

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Basic information

Entry
Database: PDB / ID: 4kc9
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 / protein ubiquitination / nuclear body / 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: 3.603 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 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase ARIH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4857
Polymers65,0921
Non-polymers3926
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.126, 96.126, 151.329
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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: 65092.223 Da / Num. of mol.: 1
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.: 6 / 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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.49M sodium citrate, 0.1M citric acid, pH 5.2, 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: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→36.47 Å / Num. all: 9319 / Num. obs: 9319 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.6→3.73 Å / % possible all: 17.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(Autosol)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(Autosol)phasing
RefinementResolution: 3.603→36.47 Å / SU ML: 0.51 / σ(F): 1.4 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.302 849 10.18 %
Rwork0.2704 --
obs0.2737 8343 90.58 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.629 Å2 / ksol: 0.291 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3035 Å2-0 Å2-0 Å2
2--2.3035 Å2-0 Å2
3----4.607 Å2
Refinement stepCycle: LAST / Resolution: 3.603→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 6 0 3139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113228
X-RAY DIFFRACTIONf_angle_d1.1964398
X-RAY DIFFRACTIONf_dihedral_angle_d20.0181095
X-RAY DIFFRACTIONf_chiral_restr0.078482
X-RAY DIFFRACTIONf_plane_restr0.004571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6031-3.82860.3898720.361606X-RAY DIFFRACTION44
3.8286-4.12380.31241510.30221367X-RAY DIFFRACTION100
4.1238-4.53810.31211360.25041397X-RAY DIFFRACTION100
4.5381-5.19320.26981710.25471357X-RAY DIFFRACTION100
5.1932-6.53670.32741560.28471374X-RAY DIFFRACTION100
6.5367-36.47160.28011630.24621393X-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)
11.1365-0.30910.14370.73130.02380.8831-0.1755-0.1669-0.30650.322-0.0406-0.1590.54020.2137-0.2950.52190.39910.0713-0.10490.10490.199858.5745.843940.4139
20.96531.47171.24943.07771.38782.21250.07760.1193-0.26820.2385-0.0841-0.5940.27750.2294-0.4690.26640.05180.1380.00570.1440.282559.537711.76130.409
30.08070.27660.00391.171-0.23280.28950.01730.1271-0.1145-0.61240.1121-0.39060.57390.1930.29590.85370.088-0.06060.0901-0.07090.286345.8424-0.91039.1465
4-0.0019-0.0829-0.06310.75090.41111.07390.1394-0.0082-0.18-0.05310.0957-0.25270.8055-0.10480.19190.7109-0.573-0.2699-0.273-0.4090.244336.5215.685-5.2904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 101:204)
2X-RAY DIFFRACTION2chain 'A' and (resseq 205:283)
3X-RAY DIFFRACTION3chain 'A' and (resseq 284:342)
4X-RAY DIFFRACTION4chain 'A' and (resseq 343:553)

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