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- PDB-3v3l: Crystal structure of human RNF146 WWE domain in complex with iso-... -

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Basic information

Entry
Database: PDB / ID: 3v3l
TitleCrystal structure of human RNF146 WWE domain in complex with iso-ADPRibose
ComponentsE3 ubiquitin-protein ligase RNF146
KeywordsLIGASE
Function / homology
Function and homology information


poly-ADP-D-ribose binding / protein autoubiquitination / protein K48-linked ubiquitination / TCF dependent signaling in response to WNT / Degradation of AXIN / RING-type E3 ubiquitin transferase / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity ...poly-ADP-D-ribose binding / protein autoubiquitination / protein K48-linked ubiquitination / TCF dependent signaling in response to WNT / Degradation of AXIN / RING-type E3 ubiquitin transferase / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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. / Zinc finger, C3HC4 type (RING finger) / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-V3L / E3 ubiquitin-protein ligase RNF146
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsWang, Z. / Cheng, Z. / Xu, W.
CitationJournal: Genes Dev. / Year: 2012
Title: Recognition of the iso-ADP-ribose moiety in poly(ADP-ribose) by WWE domains suggests a general mechanism for poly(ADP-ribosyl)ation-dependent ubiquitination.
Authors: Wang, Z. / Michaud, G.A. / Cheng, Z. / Zhang, Y. / Hinds, T.R. / Fan, E. / Cong, F. / Xu, W.
History
DepositionDec 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release

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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: E3 ubiquitin-protein ligase RNF146
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6294
Polymers20,5102
Non-polymers1,1192
Water2,234124
1
A: E3 ubiquitin-protein ligase RNF146
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8152
Polymers10,2551
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase RNF146
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8152
Polymers10,2551
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.343, 55.343, 146.471
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-91-

HOH

21A-188-

HOH

31B-184-

HOH

41B-196-

HOH

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Components

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


Mass: 10255.229 Da / Num. of mol.: 2 / Fragment: WWE domain residues 100-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF146 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NTX7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 295 K / pH: 8
Details: 45% PEG 400, 100 mM Tris HCl pH 8.0, 10 mM DTT, 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: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2011
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.63→20 Å / Num. obs: 32399
Reflection shellResolution: 1.63→1.68 Å / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.309 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1575 5.1 %RANDOM
Rwork0.151 ---
obs0.153 29606 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.47 Å20 Å2
2---0.95 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 72 124 1618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211648
X-RAY DIFFRACTIONr_bond_other_d0.0010.021176
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9942245
X-RAY DIFFRACTIONr_angle_other_deg0.81532813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12122.6694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76615291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4711522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021866
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02392
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_it3.4064898
X-RAY DIFFRACTIONr_mcbond_other1.394372
X-RAY DIFFRACTIONr_mcangle_it5.2861443
X-RAY DIFFRACTIONr_scbond_it5.7826750
X-RAY DIFFRACTIONr_scangle_it8.22710800
X-RAY DIFFRACTIONr_rigid_bond_restr1.79532824
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 130 -
Rwork0.182 2059 -
obs--97.2 %
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)
10.42360.2975-0.0120.7695-0.27411.077-0.04730.0416-0.0001-0.06150.0245-0.0045-0.0203-0.00130.02280.0212-0.00450.00180.0088-0.00460.006427.026564.835183.971
20.5410.1592-0.470.95280.08740.84470.0506-0.02040.01240.1131-0.07330.04650.0185-0.02340.02270.0255-0.01640.00620.0182-0.00770.007413.877241.757486.3183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A101 - 183
2X-RAY DIFFRACTION2B99 - 183

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