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- PDB-9bks: Crystal structure of the Human TRIP12 WWE domain (isoform 2) in c... -

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Basic information

Entry
Database: PDB / ID: 9bks
TitleCrystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ADP
ComponentsIsoform 2 of E3 ubiquitin-protein ligase TRIP12
KeywordsLIGASE / TRIP12 / Isoform 2 / WWE / SGC / Structural Genomics Consortium / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


: / negative regulation of double-strand break repair / regulation of double-strand break repair / HECT-type E3 ubiquitin transferase / nuclear thyroid hormone receptor binding / regulation of embryonic development / protein polyubiquitination / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process ...: / negative regulation of double-strand break repair / regulation of double-strand break repair / HECT-type E3 ubiquitin transferase / nuclear thyroid hormone receptor binding / regulation of embryonic development / protein polyubiquitination / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / nuclear speck / DNA repair / DNA damage response / nucleoplasm / nucleus / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase HECTD1/TRIP12-like / WWE domain superfamily / WWE domain / WWE domain profile. / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / E3 ubiquitin-protein ligase TRIP12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsKimani, S. / Dong, A. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ADP
Authors: Kimani, S. / Dong, A. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
SupersessionJul 31, 2024ID: 7UW7
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of E3 ubiquitin-protein ligase TRIP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5182
Polymers9,0911
Non-polymers4271
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.371, 33.671, 66.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isoform 2 of E3 ubiquitin-protein ligase TRIP12 / E3 ubiquitin-protein ligase for Arf / ULF / HECT-type E3 ubiquitin transferase TRIP12 / Thyroid ...E3 ubiquitin-protein ligase for Arf / ULF / HECT-type E3 ubiquitin transferase TRIP12 / Thyroid receptor-interacting protein 12 / TR-interacting protein 12 / TRIP-12


Mass: 9090.911 Da / Num. of mol.: 1 / Fragment: WWE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIP12, KIAA0045, ULF / Production host: Escherichia coli (E. coli)
References: UniProt: Q14669-2, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.87 Å3/Da / Density % sol: 34.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350, 0.1 M Sodium Hepes, MOPS pH 7.5, 0.09 M Sodium nitrate, 0.09 M Sodium phosphate dibasic, 0.09 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. obs: 23321 / % possible obs: 98.3 % / Redundancy: 6.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Χ2: 1.187 / Net I/σ(I): 11.5 / Num. measured all: 153097
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.17-1.193.30.2149360.9270.9810.1290.2510.81383
1.19-1.214.20.21510960.9510.9870.1130.2440.81691.9
1.21-1.245.70.20911290.9660.9910.0930.230.77398.6
1.24-1.266.50.19211580.9760.9940.0790.2080.7797.6
1.26-1.296.80.18211530.9770.9940.0740.1970.77399.7
1.29-1.327.10.15511530.9790.9950.0620.1680.8198.7
1.32-1.3570.13611520.9890.9970.0550.1470.69699.6
1.35-1.3970.12211900.9890.9970.0490.1310.71899.7
1.39-1.436.70.10711490.9930.9980.0440.1160.69699.7
1.43-1.476.40.09111690.9920.9980.0380.0990.75199
1.47-1.537.30.08111780.9950.9990.0320.0870.813100
1.53-1.597.30.07411660.9950.9990.0290.080.904100
1.59-1.667.20.06711880.9950.9990.0270.0730.97999.7
1.66-1.757.10.0611870.9970.9990.0240.0651.11199.7
1.75-1.866.80.05511690.9960.9990.0230.061.30199.7
1.86-26.10.0511920.9970.9990.0210.0541.60199.1
2-2.27.30.04811960.9980.9990.0190.0521.79399.8
2.2-2.527.30.04712190.9970.9990.0190.0512.037100
2.52-3.1870.04412290.99810.0180.0482.21699.8
3.18-506.30.04213120.9970.9990.0180.0462.65398.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→30.05 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.983 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17251 1134 4.9 %RANDOM
Rwork0.14978 ---
obs0.15089 22138 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.591 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2---0.61 Å20 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.17→30.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms590 0 27 77 694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012712
X-RAY DIFFRACTIONr_bond_other_d0.0010.016638
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.784986
X-RAY DIFFRACTIONr_angle_other_deg0.5971.7911467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.434591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.8858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76510115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02914
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02185
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_it3.2751.077334
X-RAY DIFFRACTIONr_mcbond_other3.2621.076334
X-RAY DIFFRACTIONr_mcangle_it5.0381.926429
X-RAY DIFFRACTIONr_mcangle_other5.0371.933430
X-RAY DIFFRACTIONr_scbond_it3.961.246378
X-RAY DIFFRACTIONr_scbond_other3.9591.246378
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0822.195556
X-RAY DIFFRACTIONr_long_range_B_refined12.50613.09803
X-RAY DIFFRACTIONr_long_range_B_other11.48412.52782
X-RAY DIFFRACTIONr_rigid_bond_restr3.14531350
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.17→1.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 85 -
Rwork0.175 1379 -
obs--84.82 %

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