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- PDB-5udh: HHARI/ARIH1-UBCH7~Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5udh
TitleHHARI/ARIH1-UBCH7~Ubiquitin
Components
  • E3 ubiquitin-protein ligase ARIH1
  • Ubiquitin C variant
  • Ubiquitin-conjugating enzyme E2 L3
KeywordsTRANSFERASE / E2 ligase / RBR E3 ligase / ubiquitin / heterotrimer
Function / homology
Function and homology information


PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / cell cycle phase transition / Lewy body / ubiquitin-protein transferase activator activity / RBR-type E3 ubiquitin transferase / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / Modulation of host responses by IFN-stimulated genes / positive regulation of protein targeting to mitochondrion ...PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / cell cycle phase transition / Lewy body / ubiquitin-protein transferase activator activity / RBR-type E3 ubiquitin transferase / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / Modulation of host responses by IFN-stimulated genes / positive regulation of protein targeting to mitochondrion / cellular response to glucocorticoid stimulus / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / RSV-host interactions / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / Cajal body / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
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 / IBR domain / In Between Ring fingers ...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 / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ring finger / Four Helix Bundle (Hemerythrin (Met), subunit A) / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 L3 / Ubiquitin C variant / E3 ubiquitin-protein ligase ARIH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.24 Å
AuthorsMiller, D.J. / Schulman, B.A.
CitationJournal: Structure / Year: 2017
Title: Structural Studies of HHARI/UbcH7Ub Reveal Unique E2Ub Conformational Restriction by RBR RING1.
Authors: Dove, K.K. / Olszewski, J.L. / Martino, L. / Duda, D.M. / Wu, X.S. / Miller, D.J. / Reiter, K.H. / Rittinger, K. / Schulman, B.A. / Klevit, R.E.
History
DepositionDec 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase ARIH1
C: Ubiquitin-conjugating enzyme E2 L3
B: E3 ubiquitin-protein ligase ARIH1
D: Ubiquitin-conjugating enzyme E2 L3
E: Ubiquitin C variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,61717
Polymers156,8325
Non-polymers78512
Water00
1
A: E3 ubiquitin-protein ligase ARIH1
C: Ubiquitin-conjugating enzyme E2 L3
E: Ubiquitin C variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5119
Polymers83,1193
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase ARIH1
D: Ubiquitin-conjugating enzyme E2 L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1068
Polymers73,7132
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.571, 76.788, 147.724
Angle α, β, γ (deg.)90.00, 107.33, 90.00
Int Tables number5
Space group name H-MC121

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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: 55653.367 Da / Num. of mol.: 2 / Fragment: UNP residues 90-557
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-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9Y4X5, Transferases; Acyltransferases; Aminoacyltransferases
#2: Protein Ubiquitin-conjugating enzyme E2 L3 / E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin- ...E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin-protein ligase L3


Mass: 18059.760 Da / Num. of mol.: 2 / Fragment: UNP residues 1-154 / Mutation: C86K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L3, UBCE7, UBCH7
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P68036, E2 ubiquitin-conjugating enzyme
#3: Protein Ubiquitin C variant


Mass: 9405.710 Da / Num. of mol.: 1 / Fragment: UNP residues 17-92
Source method: isolated from a genetically manipulated source
Details: Hexa-his N-terminal tagged protein / Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q59EM9, UniProt: P0CG48*PLUS
#4: 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: 3.45 Å3/Da / Density % sol: 64.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 ul protein mixture with 10-12 mg/ml protein in 25 mM Tris pH 7.0, 150 mM NaCl, 1 mM DTT and 1 ul well solution with 7-10% PEG 5000 MME, 0.1 M HP pH 7.0 and 5% Tascimate pH 7.0. Over 1 ml reservoir.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2016 / Details: double crystal Si(III)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.24→141.01 Å / Num. obs: 31387 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / CC1/2: 1 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.1
Reflection shellResolution: 3.24→3.45 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.76 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 3.24→141.01 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.904 / SU B: 27.258 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27906 1550 4.9 %RANDOM
Rwork0.22211 ---
obs0.22493 29836 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 116.581 Å2
Baniso -1Baniso -2Baniso -3
1-3.56 Å2-0 Å2-0.05 Å2
2--0.87 Å20 Å2
3----3.68 Å2
Refinement stepCycle: 1 / Resolution: 3.24→141.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9166 0 12 0 9178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0199430
X-RAY DIFFRACTIONr_bond_other_d0.0020.028553
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.94312792
X-RAY DIFFRACTIONr_angle_other_deg1.0193.00419528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7951159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62524.367442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.673151503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5251548
X-RAY DIFFRACTIONr_chiral_restr0.0740.21392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110750
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022230
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.82212.084675
X-RAY DIFFRACTIONr_mcbond_other6.82112.084674
X-RAY DIFFRACTIONr_mcangle_it10.76818.1185821
X-RAY DIFFRACTIONr_mcangle_other10.76818.1185822
X-RAY DIFFRACTIONr_scbond_it8.27912.2134755
X-RAY DIFFRACTIONr_scbond_other8.27912.2144756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.24118.1596971
X-RAY DIFFRACTIONr_long_range_B_refined14.65593.8210272
X-RAY DIFFRACTIONr_long_range_B_other14.65493.82410273
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.241→3.325 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 86 -
Rwork0.402 2064 -
obs--91.1 %

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