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- PDB-4qpl: Crystal structure of RNF146(RING-WWE)/UbcH5a/iso-ADPr complex -

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Basic information

Entry
Database: PDB / ID: 4qpl
TitleCrystal structure of RNF146(RING-WWE)/UbcH5a/iso-ADPr complex
Components
  • E3 ubiquitin-protein ligase RNF146
  • Ubiquitin-conjugating enzyme E2 D1
KeywordsLIGASE / Protein poly(ADP-ribosy)lation / ubiquitination / E2/E3 ubiquitin ligase / Wnt signaling / RNF146 / UbcH5a / iso-ADPR
Function / homology
Function and homology information


negative regulation of cellular response to oxidative stress / TCF dependent signaling in response to WNT / Degradation of AXIN / positive regulation of protein polyubiquitination / Regulation of PTEN stability and activity / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / poly-ADP-D-ribose binding / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects ...negative regulation of cellular response to oxidative stress / TCF dependent signaling in response to WNT / Degradation of AXIN / positive regulation of protein polyubiquitination / Regulation of PTEN stability and activity / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / poly-ADP-D-ribose binding / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / Signaling by BMP / Ub-specific processing proteases / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / negative regulation of BMP signaling pathway / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / negative regulation of TORC1 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / CDK-mediated phosphorylation and removal of Cdc6 / cellular response to hydrogen peroxide / CLEC7A (Dectin-1) signaling / Wnt signaling pathway / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / Separation of Sister Chromatids / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / Ovarian tumor domain proteases / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RNF146 / RNF146, RING finger, HC subclass / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #50 / WWE domain, subgroup / Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. / Signal recognition particle alu RNA binding heterodimer, srp9/1 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. ...E3 ubiquitin-protein ligase RNF146 / RNF146, RING finger, HC subclass / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #50 / WWE domain, subgroup / Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. / Signal recognition particle alu RNA binding heterodimer, srp9/1 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-V3L / Ubiquitin-conjugating enzyme E2 D1 / E3 ubiquitin-protein ligase RNF146
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWang, Z. / DaRosa, P.A. / Klevit, R.E. / Xu, W.
CitationJournal: Nature / Year: 2015
Title: Allosteric activation of the RNF146 ubiquitin ligase by a poly(ADP-ribosyl)ation signal.
Authors: DaRosa, P.A. / Wang, Z. / Jiang, X. / Pruneda, J.N. / Cong, F. / Klevit, R.E. / Xu, W.
History
DepositionJun 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 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 RNF146
B: Ubiquitin-conjugating enzyme E2 D1
C: E3 ubiquitin-protein ligase RNF146
D: Ubiquitin-conjugating enzyme E2 D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,13910
Polymers70,7594
Non-polymers1,3806
Water6,684371
1
A: E3 ubiquitin-protein ligase RNF146
B: Ubiquitin-conjugating enzyme E2 D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0705
Polymers35,3802
Non-polymers6903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-10 kcal/mol
Surface area15730 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase RNF146
D: Ubiquitin-conjugating enzyme E2 D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0705
Polymers35,3802
Non-polymers6903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.665, 61.688, 94.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein E3 ubiquitin-protein ligase RNF146 / Iduna / RING finger protein 146


Mass: 17857.580 Da / Num. of mol.: 2 / Fragment: UNP residues 32-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnf146 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CZW6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Ubiquitin-conjugating enzyme E2 D1 / Stimulator of Fe transport / SFT / UBC4/5 homolog / UbcH5 / Ubiquitin carrier protein D1 / ...Stimulator of Fe transport / SFT / UBC4/5 homolog / UbcH5 / Ubiquitin carrier protein D1 / Ubiquitin-conjugating enzyme E2(17)KB 1 / Ubiquitin-conjugating enzyme E2-17 kDa 1 / Ubiquitin-protein ligase D1


Mass: 17521.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A / Production host: Escherichia coli (E. coli) / References: UniProt: P51668, ubiquitin-protein ligase
#3: Chemical ChemComp-V3L / 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)


Type: RNA linking / Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.8 M sodium citrate, 80 mM Tris HCl pH7.0, 160 mM NaCl, 4 mMDTT, 20 mM trimethylamin HCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.283 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2012
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 58752 / Num. obs: 55779 / % possible obs: 94.94 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 7.8 % / Χ2: 2.348
Reflection shellResolution: 1.9→1.96 Å / Χ2: 0.807 / % possible all: 71.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.656 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2994 5.1 %RANDOM
Rwork0.1864 ---
all0.1882 58752 --
obs0.1882 55779 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.75 Å2 / Biso mean: 39.658 Å2 / Biso min: 17.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å2-0 Å2
2--6.07 Å2-0 Å2
3----3.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4886 0 76 371 5333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195116
X-RAY DIFFRACTIONr_bond_other_d0.0010.024794
X-RAY DIFFRACTIONr_angle_refined_deg1.41.986944
X-RAY DIFFRACTIONr_angle_other_deg0.793.00311066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87723.304230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19615858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1591536
X-RAY DIFFRACTIONr_chiral_restr0.0760.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215634
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021170
X-RAY DIFFRACTIONr_mcbond_it2.0123.4272428
X-RAY DIFFRACTIONr_mcbond_other2.0123.4272427
X-RAY DIFFRACTIONr_mcangle_it2.945.7483028
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)
12.0234-0.29931.56660.7871-1.51956.4481-0.0762-0.03670.08140.0421-0.0228-0.0785-0.11940.32170.0990.2238-0.0126-0.00010.14620.0030.282650.689918.155533.1286
25.49740.13961.37410.85670.2993.1919-0.08160.29410.0053-0.04090.03370.0535-0.078-0.06250.04790.2196-0.01690.03130.0254-0.01230.217920.117115.14514.2281
32.06920.14841.22541.33251.46674.6966-0.0283-0.11270.0445-0.04980.01250.0154-0.1128-0.12420.01580.2260.01140.00980.01050.01650.2448-30.440216.20114.0249
45.3275-0.24051.51450.7171-0.41823.3805-0.0229-0.4411-0.05630.03880.0082-0.0149-0.06910.06870.01470.22390.010.03360.05050.01730.2382-0.098813.84432.6713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 182
2X-RAY DIFFRACTION2B-1 - 147
3X-RAY DIFFRACTION3C30 - 182
4X-RAY DIFFRACTION4D-5 - 147

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