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- PDB-2nsq: Crystal structure of the C2 domain of the human E3 ubiquitin-prot... -

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Basic information

Entry
Database: PDB / ID: 2nsq
TitleCrystal structure of the C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like protein
ComponentsE3 ubiquitin-protein ligase NEDD4-like protein
KeywordsLIGASE / UBL-CONJUGATION PATHWAY / C2 DOMAIN / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / regulation of sodium ion transmembrane transport / negative regulation of sodium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization ...positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / regulation of sodium ion transmembrane transport / negative regulation of sodium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization / positive regulation of dendrite extension / potassium channel inhibitor activity / ventricular cardiac muscle cell action potential / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / regulation of monoatomic ion transmembrane transport / regulation of dendrite morphogenesis / regulation of membrane depolarization / protein monoubiquitination / sodium channel regulator activity / potassium channel regulator activity / protein K48-linked ubiquitination / monoatomic ion transmembrane transport / multivesicular body / Downregulation of TGF-beta receptor signaling / regulation of membrane potential / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Budding and maturation of HIV virion / regulation of protein stability / Stimuli-sensing channels / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / cell differentiation / protein ubiquitination / Golgi apparatus / extracellular exosome / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
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 / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / WW 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 / C2 domain / C2 domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
Citation
Journal: To be Published
Title: The C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like protein
Authors: Walker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
#1: Journal: Eur.J.Hum.Genet. / Year: 2001
Title: NEDD4L on human chromosome 18q21 has multiple forms of transcripts and is a homologue of the mouse Nedd4-2 gene
Authors: Chen, H. / Ross, C.A. / Wang, N. / Huo, Y. / MacKinnon, D.F. / Potash, J.B. / Simpson, S.G. / McMahon, F.J. / DePaulo Jr., J.R. / McInnis, M.G.
#2: Journal: J.Biol.Chem. / Year: 2005
Title: 14-3-3 proteins modulate the expression of epithelial Na+ channels by phosphorylation-dependent interaction with Nedd4-2 ubiquitin ligase
Authors: Ichimura, T. / Yamamura, H. / Sasamoto, K. / Tominaga, Y. / Taoka, M. / Kakiuchi, K. / Shinkawa, T. / Takahashi, N. / Shimada, S. / Isobe, T.
#3: Journal: Mol.Cell.Biol. / Year: 2000
Title: Latent membrane protein 2A of Epstein-Barr virus binds WW domain E3 protein-ubiquitin ligases that ubiquitinate B-cell tyrosine kinases
Authors: Winberg, G. / Matskova, L. / Chen, F. / Plant, P. / Rotin, D. / Gish, G. / Ingham, R. / Ernberg, I. / Pawson, T.
#4: Journal: J.Biol.Chem. / Year: 2002
Title: Serum and glucocorticoid-regulated kinase modulates Nedd4-2-mediated inhibition of the epithelial Na+ channel
Authors: Snyder, P.M. / Olson, D.R. / Thomas, B.C.
#5: Journal: J.Biol.Chem. / Year: 2002
Title: N4WBP5, a potential target for ubiquitination by the Nedd4 family of proteins, is a novel Golgi-associated protein
Authors: Harvey, K.F. / Shearwin-Whyatt, L.M. / Fotia, A. / Parton, R.G. / Kumar, S.
History
DepositionNov 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 28, 2013Group: Refinement description
Revision 1.4Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase NEDD4-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0903
Polymers17,9361
Non-polymers1542
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.930, 60.036, 74.510
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 E3 ubiquitin-protein ligase NEDD4-like protein / Nedd4-2 / NEDD4.2


Mass: 17935.568 Da / Num. of mol.: 1 / Fragment: C2 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 / Plasmid: p28a-LIC-TEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96PU5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 14% PEG 4000, 0.2 M NaOAc, pH 6.5, 1 mM DTT. 20% Ethylene glycol added as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 16, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 12925 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rsym value: 0.081 / Net I/σ(I): 23.07
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.638 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TJM

1tjm


Resolution: 1.85→27.84 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.577 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 631 4.9 %RANDOM
Rwork0.171 ---
obs0.174 12260 98.1 %-
all-12893 --
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: 21.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20 Å2
2---0.82 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 10 111 1260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221189
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9851605
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69722.98257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08315208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9321511
X-RAY DIFFRACTIONr_chiral_restr0.1370.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02899
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2463
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2786
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0573734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.81841157
X-RAY DIFFRACTIONr_scbond_it3.8735514
X-RAY DIFFRACTIONr_scangle_it5.2927448
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 37 -
Rwork0.251 762 -
obs--85.18 %
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)
110.88344.81865.076620.08492.78910.3085-0.23810.16660.4466-0.52830.1752-0.5141-0.27830.94110.06290.0926-0.02820.0360.1611-0.0150.091317.651820.62391.4952
20.0843-0.9311-0.254822.90525.78542.56460.4448-0.565-0.0974-0.51170.05720.35660.4386-1.4981-0.50210.2692-0.1490.02220.25160.07210.084211.114124.7544-8.8252
32.4759-0.7768-10.55265.83631.499145.5637-0.0735-0.53040.10680.10880.0682-0.3046-0.7382.00110.00530.0782-0.05590.00750.1633-0.02560.044713.560728.83536.4349
46.63914.1731-1.57483.89240.21045.3350.1124-0.16130.01140.2714-0.16210.2008-0.0782-0.28310.04970.12020.00410.02550.06720.00260.06884.568625.985521.943
52.4622.33-1.5938.98513.781414.85310.1743-0.3265-0.26720.7642-0.05090.56550.6815-0.4741-0.12340.0956-0.00640.01750.08610.02880.10054.903816.04721.9967
66.30690.90983.69682.2492-2.20815.7151-0.1526-0.10880.2353-0.05580.11640.0148-0.3101-0.2740.03630.0755-0.00920.01220.0778-0.01630.04993.451419.50492.3972
727.38172.8774-0.07225.06121.35686.62410.06720.1404-0.01750.0197-0.21220.0095-0.0944-0.10430.1450.156-0.0095-0.00740.075-0.00840.09030.775616.0048-2.2438
81.39310.52151.54411.62720.650317.7780.1629-0.0371-0.0760.25990.0555-0.08070.40040.6305-0.21840.06420.0099-0.02250.1293-0.00210.104111.915416.644316.8751
91.71220.4567-0.82150.79380.93554.89330.0756-0.18290.1210.15280.062-0.202-0.32910.3729-0.13760.1059-0.0064-0.01150.0767-0.01680.089111.761423.82317.4581
104.58572.4365-2.6914.5328-1.32176.9576-0.13250.46270.149-0.47210.20840.2229-0.266-0.2127-0.0760.1588-0.0168-0.01530.08180.00190.08155.059324.2858-1.2726
111.8757-0.07890.90615.2594-9.681212.92610.106-0.1358-0.28190.2282-0.01190.07690.10220.0281-0.09410.0908-0.02530.01410.1205-0.01160.15274.00315.569517.8038
127.84955.5052-2.585420.97-2.93429.30680.0143-0.2324-0.53110.8846-0.1083-0.52010.04110.25270.0940.1191-0.0063-0.01560.11510.0480.12533.57855.902321.9199
135.732-3.48314.449723.0061-16.462420.8512-0.2134-0.0016-0.3478-0.3060.26520.0642-0.0663-0.971-0.05180.060.0032-0.00320.0861-0.02110.0996-1.636320.288414.3487
1410.43393.2715-1.75628.7272.72161.6859-0.06010.13780.638-0.2092-0.06540.6496-0.5148-0.22030.12550.2740.0232-0.04620.09220.04640.0944.127632.55051.8299
1528.62437.9522-2.882125.324913.96679.72431.16320.941.74050.77310.9466-0.68770.2149-0.0482-2.10980.1736-0.0252-0.03850.12980.00130.08114.623838.46279.8472
1611.12245.838-0.946810.55710.96336.27320.0378-0.14590.062-0.3612-0.19460.428-0.1086-0.25130.15680.14340.0595-0.00870.1337-0.00990.104-1.740926.738915.0087
1743.401420.472712.104711.51595.85253.387-0.1582-0.06450.237-0.09630.10360.9372-0.1946-0.18260.05450.0599-0.0173-0.00930.2505-0.02230.1371-10.410320.587719.0691
1811.285-2.67662.44116.56642.53535.59410.07770.20410.2867-0.1116-0.09450.0972-0.59320.26770.01680.1597-0.0212-0.00510.1025-0.02450.09125.43430.362416.3059
193.84781.02-2.838313.0228-0.090414.18390.09780.19090.0008-0.66790.0536-0.6312-1.00440.5591-0.15140.2256-0.0850.03920.095400.114312.372932.86441.9698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 137 - 14
2X-RAY DIFFRACTION2AA14 - 2015 - 21
3X-RAY DIFFRACTION3AA21 - 2522 - 26
4X-RAY DIFFRACTION4AA26 - 3327 - 34
5X-RAY DIFFRACTION5AA34 - 4635 - 47
6X-RAY DIFFRACTION6AA47 - 5248 - 53
7X-RAY DIFFRACTION7AA53 - 5854 - 59
8X-RAY DIFFRACTION8AA59 - 6760 - 68
9X-RAY DIFFRACTION9AA68 - 8069 - 81
10X-RAY DIFFRACTION10AA81 - 9082 - 91
11X-RAY DIFFRACTION11AA91 - 9792 - 98
12X-RAY DIFFRACTION12AA98 - 10399 - 104
13X-RAY DIFFRACTION13AA104 - 109105 - 110
14X-RAY DIFFRACTION14AA110 - 118111 - 119
15X-RAY DIFFRACTION15AA119 - 127120 - 128
16X-RAY DIFFRACTION16AA128 - 137129 - 138
17X-RAY DIFFRACTION17AA138 - 144139 - 145
18X-RAY DIFFRACTION18AA145 - 149146 - 150
19X-RAY DIFFRACTION19AA150 - 154151 - 155

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