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- PDB-5tj7: Structure of WWP2 WW2-2,3-linker-HECT aa 334-398 linked to 485-865 -

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Basic information

Entry
Database: PDB / ID: 5tj7
TitleStructure of WWP2 WW2-2,3-linker-HECT aa 334-398 linked to 485-865
ComponentsNEDD4-like E3 ubiquitin-protein ligase WWP2
KeywordsTRANSFERASE / WWP2 / HECT Domain / WW2 / WWP1 / ITCH / autoinhibition
Function / homology
Function and homology information


negative regulation of transporter activity / negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / transcription factor binding / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle ...negative regulation of transporter activity / negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / transcription factor binding / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / protein K63-linked ubiquitination / negative regulation of Notch signaling pathway / ubiquitin ligase complex / protein autoubiquitination / regulation of membrane potential / negative regulation of DNA-binding transcription factor activity / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein modification process / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / RNA polymerase II-specific DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / protein ubiquitination / symbiont entry into host cell / negative regulation of gene expression / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. ...Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / NEDD4-like E3 ubiquitin-protein ligase WWP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, Z. / Gabelli, S.B.
CitationJournal: Mol. Cell / Year: 2017
Title: A Tunable Brake for HECT Ubiquitin Ligases.
Authors: Chen, Z. / Jiang, H. / Xu, W. / Li, X. / Dempsey, D.R. / Zhang, X. / Devreotes, P. / Wolberger, C. / Amzel, L.M. / Gabelli, S.B. / Cole, P.A.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 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 / diffrn_radiation_wavelength / 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEDD4-like E3 ubiquitin-protein ligase WWP2
B: NEDD4-like E3 ubiquitin-protein ligase WWP2
C: NEDD4-like E3 ubiquitin-protein ligase WWP2
D: NEDD4-like E3 ubiquitin-protein ligase WWP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,9299
Polymers213,7664
Non-polymers1635
Water17,943996
1
A: NEDD4-like E3 ubiquitin-protein ligase WWP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4652
Polymers53,4421
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NEDD4-like E3 ubiquitin-protein ligase WWP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4652
Polymers53,4421
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NEDD4-like E3 ubiquitin-protein ligase WWP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5002
Polymers53,4421
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NEDD4-like E3 ubiquitin-protein ligase WWP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5003
Polymers53,4421
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.000, 73.907, 82.380
Angle α, β, γ (deg.)89.990, 89.660, 90.010
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NEDD4-like E3 ubiquitin-protein ligase WWP2 / Atrophin-1-interacting protein 2 / AIP2 / HECT-type E3 ubiquitin transferase WWP2 / WW domain- ...Atrophin-1-interacting protein 2 / AIP2 / HECT-type E3 ubiquitin transferase WWP2 / WW domain-containing protein 2


Mass: 53441.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWP2 / Plasmid: pGEX6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus
References: UniProt: O00308, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 996 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M potassium thiocyanate, 30% PEG monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5417 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 47592 / % possible obs: 91.2 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.044 / Rrim(I) all: 0.069 / Χ2: 3.418 / Net I/σ(I): 16.6 / Num. measured all: 101067
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.641.80.13114740.9280.1180.1772.43255.4
2.64-2.691.80.13116140.9270.1140.1742.70362.9
2.69-2.741.90.12319290.9380.1070.1642.19972.4
2.74-2.820.11322180.950.0970.1492.38287.5
2.8-2.862.10.10324150.9670.0850.1341.91491.2
2.86-2.932.10.0923990.9710.0750.1182.3292.9
2.93-32.10.08624700.9690.0730.1132.15193.5
3-3.082.10.07824210.9730.0660.1032.57293.6
3.08-3.172.20.07324590.9790.060.0952.61794.3
3.17-3.282.20.06124540.9820.0520.0812.45494.9
3.28-3.392.20.05925370.980.0490.0773.13896.3
3.39-3.532.20.05725620.980.0480.0754.22997.3
3.53-3.692.20.05125590.9850.0430.0673.90998.2
3.69-3.882.30.04825590.9870.0410.0634.33798.8
3.88-4.132.20.04626040.990.0380.063.72698.7
4.13-4.452.20.04425460.990.0370.0584.22498.8
4.45-4.892.20.0425900.9920.0330.0524.03899.2
4.89-5.62.20.04325690.9890.0360.0564.5599.3
5.6-7.052.10.04826210.9860.0410.0635.25899.6
7.05-5020.03325920.9960.0280.0444.91599.4

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TJQ

5tjq


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.82 / WRfactor Rfree: 0.2836 / WRfactor Rwork: 0.2072 / FOM work R set: 0.8045 / SU B: 13.025 / SU ML: 0.286 / SU Rfree: 0.4633 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 2310 4.9 %RANDOM
Rwork0.2072 ---
obs0.2108 44712 90.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.4 Å2 / Biso mean: 23.905 Å2 / Biso min: 6.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.19 Å2-0.21 Å2
2---0.07 Å20.14 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14911 0 7 996 15914
Biso mean--31.34 36.68 -
Num. residues----1761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01915322
X-RAY DIFFRACTIONr_bond_other_d0.0080.0214150
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.93920673
X-RAY DIFFRACTIONr_angle_other_deg1.236332496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.78851753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86923.385845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.989152725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.65715128
X-RAY DIFFRACTIONr_chiral_restr0.1270.22081
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217321
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023975
LS refinement shellResolution: 2.601→2.669 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 113 -
Rwork0.281 2021 -
all-2134 -
obs--54.82 %

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