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- PDB-2oni: Catalytic Domain of the Human NEDD4-like E3 Ligase -

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Basic information

Entry
Database: PDB / ID: 2oni
TitleCatalytic Domain of the Human NEDD4-like E3 Ligase
ComponentsE3 ubiquitin-protein ligase NEDD4-like protein
KeywordsLIGASE / ALPHA and BETA PROTEIN (a + b) / E3 LIGASE / HECT DOMAIN / UBL-CONJUGATION PATHWAY / 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 / regulation of protein stability / Budding and maturation of HIV virion / 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
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / 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, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / 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 / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: NEDD4-like E3 Ubiquitin-protein Ligase
Authors: Walker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionJan 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,2712
Polymers47,2481
Non-polymers231
Water2,144119
1
A: E3 ubiquitin-protein ligase NEDD4-like protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)94,5414
Polymers94,4952
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area4430 Å2
ΔGint-38 kcal/mol
Surface area34750 Å2
MethodPISA
2
A: E3 ubiquitin-protein ligase NEDD4-like protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)283,62312
Polymers283,4856
Non-polymers1386
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area19620 Å2
ΔGint-137 kcal/mol
Surface area97930 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.058, 103.058, 182.214
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe second part of the biological assembly is generated by the two fold axis: x,x-y,-z+1/2.

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Components

#1: Protein E3 ubiquitin-protein ligase NEDD4-like protein / Nedd4-2 / NEDD4.2 / NEDD4-like ubiquitin-protein ligase / neural precursor cell expressed / ...Nedd4-2 / NEDD4.2 / NEDD4-like ubiquitin-protein ligase / neural precursor cell expressed / developmentally down-regulated 4-like / ubiquitin-protein ligase NEDD4-like / developmentally down-regulated gene 4-like / ubiquitin-protein ligase Rsp5


Mass: 47247.531 Da / Num. of mol.: 1 / Fragment: Hect Domain (ubiquitin transferase)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 / Plasmid: pET28a-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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.95 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: THE PROTEIN WAS DISSOLVED AT 10 mg/mL IN 10 mM TRIS-HCL, PH 8.0, 100 mM NaCl, 2% GLYCEROL AND 1 mM DTT. CRYSTALS WERE GROWN BY VAPOR DIFFUSION, HANGING DROPS BY MIXING 2 MICROL PROTEIN ...Details: THE PROTEIN WAS DISSOLVED AT 10 mg/mL IN 10 mM TRIS-HCL, PH 8.0, 100 mM NaCl, 2% GLYCEROL AND 1 mM DTT. CRYSTALS WERE GROWN BY VAPOR DIFFUSION, HANGING DROPS BY MIXING 2 MICROL PROTEIN SOLUTION WITH 2 MICROL WELL SOLUTION (1.7 M SODIUM/POTASSIUM PHOSPHATE, PH 6.0, 1 mM DTT) AT TEMPERATURE 294.0K. FOR CRYOPROTECTION, THE CRYSTALS WERE SOAKED IN 2 M SODIUM-POTASSIUM PHOSPHATE, pH 7.0, 1 mM DTT, 25% ETHYLENE GLYCOL AND 2 mG/mL SEMETNEDD4L.574.947.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 9, 2006 / Details: mirror
RadiationMonochromator: cryogenically-cooled Si(111) double-crystal system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 29656 / Num. obs: 29656 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Rsym value: 0.091 / Net I/σ(I): 35.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2878 / Rsym value: 0.84 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→28.28 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.098 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.198
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.25916 1534 5.2 %RANDOM
Rwork0.20632 ---
obs0.20896 28067 99.62 %-
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: 44.493 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.11 Å20 Å2
2---0.21 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 1 119 3241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223227
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9534366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2555379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57323.895172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58815552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9871522
X-RAY DIFFRACTIONr_chiral_restr0.1230.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022514
X-RAY DIFFRACTIONr_nbd_refined0.2140.21422
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22185
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.214
X-RAY DIFFRACTIONr_mcbond_it1.98231890
X-RAY DIFFRACTIONr_mcangle_it3.05143049
X-RAY DIFFRACTIONr_scbond_it4.77951395
X-RAY DIFFRACTIONr_scangle_it6.44171317
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 102 -
Rwork0.218 1999 -
obs--99.39 %
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)
112.41080.08682.92567.0261-0.395313.2238-0.4705-0.15070.0302-0.08220.35530.72780.1024-1.09590.1151-0.1042-0.1604-0.0348-0.1044-0.0803-0.009820.7551-1.55728.3163
210.66574.5535-2.34553.665-0.47680.6758-0.50380.267-1.4198-0.49480.2004-0.78570.78060.38760.3034-0.0388-0.00380.1693-0.0177-0.0840.031840.4319-2.856420.2299
313.8757-1.35560.70715.42265.001810.1241-0.1382-1.0408-0.5227-0.09750.6821-0.25480.58940.6845-0.5439-0.14330.03190.0060.3233-0.1578-0.068452.275112.603127.3664
45.0324-3.8128-2.24711.29995.22911.9262-0.0385-0.30310.7266-0.16910.5804-0.7227-0.8741.1894-0.5419-0.1739-0.1894-0.00790.0938-0.0580.054446.902722.457225.8022
58.2062-3.1649-2.76277.79352.00245.7063-0.7462-0.2234-0.62020.31610.7611-0.28680.53780.3296-0.0149-0.13-0.00250.06010.089-0.06180.005148.37819.333822.6907
68.6995-0.7775-1.009311.31-4.530410.3884-0.8784-0.9265-0.33831.13190.4367-0.76650.18470.4520.4417-0.0346-0.01070.01320.0144-0.0544-0.050542.867314.601833.6976
74.38691.19790.82043.05441.00554.8386-0.2013-0.16790.19280.00310.15780.1659-0.11230.13530.0435-0.1072-0.0538-0.0894-0.05950.0424-0.081527.876625.638823.9102
82.5393-0.1883-0.61273.652-1.54692.5857-0.13290.1447-0.0002-0.18440.1015-0.1559-0.0561-0.0030.0314-0.013-0.1482-0.01990.045-0.0106-0.05933.404117.9519.1085
912.3525-5.42650.23944.4625-0.53492.06960.15010.0449-0.6011-0.32460.01360.56980.0253-0.2884-0.1637-0.0755-0.1608-0.12310.05960.0378-0.086217.347914.113213.6871
1020.9688-4.92326.46111.2909-1.41714.5667-0.3216-1.5948-0.31750.15560.52120.1539-0.3043-0.8156-0.1996-0.1075-0.0502-0.0550.32340.0766-0.0385.391723.06717.6543
1121.42273.5034-5.24925.056-1.58964.8757-0.1162-0.29561.16830.2210.34680.7684-0.2018-1.018-0.2306-0.03970.0638-0.08790.17580.0164-0.09311.401931.21117.3363
128.76221.32856.50660.55452.02527.887-0.2960.05191.3156-0.0867-0.20110.0794-0.78920.03370.49710.0545-0.0011-0.129-0.05660.04280.048717.21135.45817.0517
1326.72911.5321-2.990523.536-5.4559.11390.743-0.43271.03120.2386-0.02442.0651-0.1256-1.4662-0.7186-0.00020.0327-0.14930.36940.0295-0.01911.311927.17861.975
149.9029-3.16023.53091.7936-0.17062.61050.03380.27920.0453-0.3118-0.01190.09310.0977-0.1678-0.022-0.0124-0.0829-0.11550.03410.0691-0.173117.273822.89638.6933
155.13980.96240.50469.60940.27183.7026-0.23820.4158-0.6002-0.71620.1924-0.46470.59290.03150.04580.018-0.13910.01310.0373-0.0799-0.107534.5868.734613.268
161.6705-1.2429-2.13944.25775.15467.0346-0.3384-0.0425-0.03740.02970.16150.36720.22210.36430.177-0.1155-0.093-0.0347-0.04730.0824-0.047223.838116.404235.8544
172.6872-0.0289-1.30372.1513-0.08077.039-0.05990.16370.0627-0.306-0.1270.0191-0.13830.30940.1869-0.1694-0.0312-0.02430.01770.02760.022619.019524.936144.2222
186.95-0.36741.05123.50192.53064.325-0.0872-0.31710.5741-0.0804-0.08440.5213-0.5806-0.20460.1717-0.08210.0303-0.0551-0.04890.040.120611.392332.469549.8233
194.8902-1.1394-1.28771.77921.57784.11920.19890.18450.7823-0.27960.02840.5165-0.6843-0.3794-0.2273-0.17770.0218-0.0884-0.11320.01170.059510.214531.25447.3444
207.69421.16042.37676.5202-3.572512.6968-0.070.5288-0.2594-0.157-0.01310.72060.5127-0.47520.0831-0.2628-0.0237-0.08470.0845-0.06530.16856.525819.69147.7146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA569 - 58114 - 26
2X-RAY DIFFRACTION2AA582 - 59627 - 41
3X-RAY DIFFRACTION3AA597 - 60242 - 47
4X-RAY DIFFRACTION4AA603 - 61448 - 59
5X-RAY DIFFRACTION5AA615 - 63260 - 77
6X-RAY DIFFRACTION6AA633 - 65478 - 99
7X-RAY DIFFRACTION7AA655 - 675100 - 120
8X-RAY DIFFRACTION8AA676 - 717121 - 162
9X-RAY DIFFRACTION9AA718 - 729163 - 174
10X-RAY DIFFRACTION10AA730 - 746175 - 191
11X-RAY DIFFRACTION11AA747 - 756192 - 201
12X-RAY DIFFRACTION12AA757 - 776202 - 221
13X-RAY DIFFRACTION13AA777 - 783222 - 228
14X-RAY DIFFRACTION14AA784 - 804229 - 249
15X-RAY DIFFRACTION15AA805 - 820250 - 265
16X-RAY DIFFRACTION16AA821 - 851266 - 296
17X-RAY DIFFRACTION17AA852 - 902297 - 347
18X-RAY DIFFRACTION18AA903 - 915348 - 360
19X-RAY DIFFRACTION19AA916 - 933361 - 378
20X-RAY DIFFRACTION20AA934 - 946379 - 391

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