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- PDB-5tte: Crystal Structure of an RBR E3 ubiquitin ligase in complex with a... -

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Basic information

Entry
Database: PDB / ID: 5tte
TitleCrystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub thioester intermediate mimic
Components
  • E3 ubiquitin-protein ligase ARIH1
  • Ubiquitin-conjugating enzyme E2 L3
  • ubiquitin
KeywordsLIGASE / RBR E3 ubiquitin ligase / E2 / complex / transthioloation / TRANSFERASE
Function / homology
Function and homology information


PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / Lewy body / RBR-type E3 ubiquitin transferase / cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity ...PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / Lewy body / RBR-type E3 ubiquitin transferase / cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / ubiquitin conjugating enzyme activity / Cajal body / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / Regulation of TNFR1 signaling / protein modification process / PKR-mediated signaling / Regulation of necroptotic cell death / ISG15 antiviral mechanism / modification-dependent protein catabolic process / protein polyubiquitination / protein tag activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / presynapse / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process / cell population proliferation / transcription coactivator activity / nuclear body / protein ubiquitination / mRNA binding / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / 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. / 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, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / 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
: / Ubiquitin-conjugating enzyme E2 L3 / Ubiquitin / E3 ubiquitin-protein ligase ARIH1
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.501 Å
AuthorsYuan, L. / Lv, Z. / Olsen, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115568-02 United States
CitationJournal: Nat Commun / Year: 2017
Title: Structural insights into the mechanism and E2 specificity of the RBR E3 ubiquitin ligase HHARI.
Authors: Yuan, L. / Lv, Z. / Atkison, J.H. / Olsen, S.K.
History
DepositionNov 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.classification
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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
B: E3 ubiquitin-protein ligase ARIH1
E: Ubiquitin-conjugating enzyme E2 L3
F: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0799
Polymers93,6863
Non-polymers3926
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-12 kcal/mol
Surface area36680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.234, 154.234, 285.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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: 64284.855 Da / Num. of mol.: 1 / Fragment: unp residues 1-557
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARIH1, ARI, MOP6, UBCH7BP, HUSSY-27 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): codon plus
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: 19426.289 Da / Num. of mol.: 1 / Fragment: unp residues 1-154 / Mutation: C17S, C86K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L3, UBCE7, UBCH7 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): codon plus
References: UniProt: P68036, E2 ubiquitin-conjugating enzyme
#3: Protein ubiquitin /


Mass: 9975.218 Da / Num. of mol.: 1 / Fragment: unp residues 1-76
Mutation: K6R, K11R, K27R, S28A, K29R, K33R, K48R, S57A, K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): codon plus / References: UniProt: A0A1D6DHW0, UniProt: P69326*PLUS
#4: 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: 5.23 Å3/Da / Density % sol: 76.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.17
Details: 0.1M Sodium Cacodylate pH6.17, 0.35M Sodium Acetate, 10% Glycerol

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 24762 / % possible obs: 95 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.41

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KBC

4kbc


Resolution: 3.501→49.714 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 25.06 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 1999 8.08 %random
Rwork0.2263 ---
obs0.2284 24742 95.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.501→49.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 6 0 5548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055696
X-RAY DIFFRACTIONf_angle_d0.5047654
X-RAY DIFFRACTIONf_dihedral_angle_d13.2913465
X-RAY DIFFRACTIONf_chiral_restr0.039804
X-RAY DIFFRACTIONf_plane_restr0.003995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5009-3.58840.39921150.35791301X-RAY DIFFRACTION78
3.5884-3.68540.34121280.34571468X-RAY DIFFRACTION88
3.6854-3.79380.35631350.31281529X-RAY DIFFRACTION92
3.7938-3.91620.37311390.2941578X-RAY DIFFRACTION94
3.9162-4.05610.31461400.26331598X-RAY DIFFRACTION94
4.0561-4.21850.26081390.24551579X-RAY DIFFRACTION95
4.2185-4.41030.25831460.21681657X-RAY DIFFRACTION98
4.4103-4.64270.21081450.20781646X-RAY DIFFRACTION98
4.6427-4.93330.2261460.18771672X-RAY DIFFRACTION98
4.9333-5.31390.21411480.19091680X-RAY DIFFRACTION98
5.3139-5.84790.27221490.22271687X-RAY DIFFRACTION99
5.8479-6.69230.28261500.231719X-RAY DIFFRACTION99
6.6923-8.42490.24761530.21651744X-RAY DIFFRACTION99
8.4249-49.71870.18421660.18691885X-RAY DIFFRACTION99
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)
11.0441-0.67140.54392.13690.09440.7960.02460.0194-0.09-0.1785-0.0427-0.1174-0.03240.2357-00.6403-0.1390.06331.0757-0.13350.8799-7.844275.1493135.649
21.81560.2260.64120.77980.04810.2397-1.1687-1.20340.5374-0.548-0.0319-0.0206-0.9805-0.6641-0.89910.42260.4861-0.28591.9619-0.16911.26530.514674.6536141.8536
30.1952-0.1460.05220.46280.31330.1443-0.10710.3529-0.0666-0.12890.03790.0813-0.0591-0.4361-0.00020.87110.194-0.0751.42410.09581.056744.762567.0051135.1545
41.1656-0.33960.15570.9037-0.45150.17410.23230.24520.4286-0.558-0.3227-0.12520.04910.34070.18051.03130.1549-0.02651.753-0.13811.093930.558166.6915131.9451
51.17550.032-0.1650.6343-0.37820.1278-0.35790.3367-0.50690.05860.13230.4174-0.0302-0.0607-0.18590.84170.3216-0.05471.3805-0.08481.09330.794754.6881133.6555
60.2356-0.18150.0990.93960.66610.9055-0.6485-0.30380.37360.5713-0.15680.2198-1.2465-0.5806-0.15781.88930.1571-0.42060.22520.12530.9328-9.8572111.0709129.4833
70.27890.00240.13730.0010.01870.1213-0.45630.64660.41150.40690.1012-0.7057-0.76550.4199-0.17532.2738-1.02070.2414-0.0646-0.20161.0552-2.6172115.145136.6331
80.40720.0948-0.00960.6453-0.03830.7040.11790.0209-0.1313-0.5609-0.0503-0.0632-1.41130.186-0.01191.0716-0.47450.10620.8391-0.08150.9027-0.1795109.4017144.8057
90.00250.01820.01590.04380.01330.00140.03610.28130.08970.2798-0.1096-0.6693-0.06820.34750.00021.2963-0.0109-0.16421.41410.13311.30075.1763105.1201152.1345
100.1970.2805-0.18830.1706-0.05650.13-0.2593-0.0214-0.08720.2637-0.29580.9446-0.02020.3119-0.00020.983-0.43010.03451.1667-0.03750.8034-7.0706101.4554143.3358
110.05010.0185-0.02230.0372-0.01580.04421.17020.2376-1.17880.2510.32480.335-0.39330.5310.00151.3507-0.2248-0.18391.24670.01231.19660.0923102.1307162.0632
120.2024-0.3269-0.18860.09260.06940.1645-0.49150.31030.39770.07930.4865-0.0573-0.63380.444201.323-0.2229-0.0611.01470.02751.0740.7124118.2499158.5118
13-0.01480.0423-0.12860.528-0.81191.24410.3362-0.4346-0.069-0.3999-0.6538-0.26151.1579-0.34820.00510.5342-0.16950.08321.9794-0.15621.0374-34.112993.8649156.6913
140.1676-0.049-0.1260.4236-0.03360.09380.6734-0.6486-0.07170.4656-0.9271-0.0613-0.92140.523-0.00010.9834-0.2398-0.02941.539-0.11920.955-24.345891.2803157.5024
150.0799-0.0295-0.09790.3121-0.13050.01350.4247-0.33840.0424-0.2081-0.09330.195-0.60120.37260.00011.02950.0370.13831.3141-0.24011.1285-26.2324100.121152.4463
16-0.00160.0084-0.00310.00820.00540.0015-0.61470.05850.0037-0.1445-0.43450.1508-0.1043-0.25520.00110.9251-0.3574-0.04451.7127-0.22491.1962-8.0391.4062149.2917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 100 through 316 )
2X-RAY DIFFRACTION2chain 'B' and (resid 317 through 349 )
3X-RAY DIFFRACTION3chain 'B' and (resid 350 through 402 )
4X-RAY DIFFRACTION4chain 'B' and (resid 403 through 450 )
5X-RAY DIFFRACTION5chain 'B' and (resid 451 through 554 )
6X-RAY DIFFRACTION6chain 'E' and (resid 4 through 17 )
7X-RAY DIFFRACTION7chain 'E' and (resid 18 through 39 )
8X-RAY DIFFRACTION8chain 'E' and (resid 40 through 75 )
9X-RAY DIFFRACTION9chain 'E' and (resid 76 through 85 )
10X-RAY DIFFRACTION10chain 'E' and (resid 86 through 113 )
11X-RAY DIFFRACTION11chain 'E' and (resid 114 through 132 )
12X-RAY DIFFRACTION12chain 'E' and (resid 133 through 154 )
13X-RAY DIFFRACTION13chain 'F' and (resid -2 through 6 )
14X-RAY DIFFRACTION14chain 'F' and (resid 7 through 45 )
15X-RAY DIFFRACTION15chain 'F' and (resid 46 through 71 )
16X-RAY DIFFRACTION16chain 'F' and (resid 72 through 76 )

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