PDB-3b7y: Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Li...

ID or keywords:

Entry

Database: PDB / ID: 3b7y

Title

Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4

Components

E3 ubiquitin-protein ligase NEDD4

Keywords

LIGASE /

C2 DOMAIN / UBL-CONJUGATION PATHWAY /

STRUCTURAL GENOMICS CONSORTIUM / SGC /

Cytoplasm / Host-virus interaction /

Phosphorylation / Polymorphism / Ubl conjugation pathway

Function / homology

Function and homology information

formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity /

viral budding / intracellular glucocorticoid receptor signaling pathway / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome ...formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity /

viral budding / intracellular glucocorticoid receptor signaling pathway / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome / apicolateral plasma membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase /

sodium channel inhibitor activity / proline-rich region binding / regulation of monoatomic ion transmembrane transport /

RNA polymerase binding / lysosomal transport /

beta-2 adrenergic receptor binding / neuromuscular junction development / regulation of dendrite morphogenesis / regulation of synapse organization / negative regulation of vascular endothelial growth factor receptor signaling pathway / progesterone receptor signaling pathway / protein K63-linked ubiquitination / phosphoserine residue binding /

regulation of macroautophagy /

ubiquitin ligase complex / Downregulation of ERBB4 signaling / Regulation of PTEN localization /

ubiquitin binding /

regulation of membrane potential /

receptor internalization / ISG15 antiviral mechanism / Regulation of PTEN stability and activity / response to calcium ion / positive regulation of protein catabolic process / cellular response to UV / neuron projection development /

ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation /

cell cortex / ubiquitin-dependent protein catabolic process /

dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / protein domain specific binding /

innate immune response / DNA damage response /

chromatin / perinuclear region of cytoplasm /

Golgi apparatus /

enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome /

nucleus /

plasma membrane /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Walker, J.R. / Ruzanov, M. / Butler-Cole, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)

Citation

Journal: To be Published
Title: C2 Domain of the Human E3 Ubiquitin-Protein Ligase NEDD4.
Authors: Walker, J.R. / Ruzanov, M. / Butler-Cole, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.

History

Deposition	Oct 31, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 27, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 30, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3b7y.cif.gz	137.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3b7y.ent.gz	107.6 KB	Display	PDB format
PDBx/mmJSON format	3b7y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b7/3b7y ftp://data.pdbj.org/pub/pdb/validation_reports/b7/3b7y	HTTPS FTP

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Related structure data

Related structure data	2nsqS S: Starting model for refinement
Similar structure data	5wez-d 1ulo-d 4d0q-d 3vk6-d 1wrz-d 3cp3-d 3l6j-2 2nsq-d 5sv2-d 4bjt-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#245 - May 2020 Spliceosomes similarity (6) #60 - Dec 2004 Ubiquitin similarity (2) #234 - Jun 2019 MDM2 and Cancer similarity (2) #148 - Apr 2012 Ras Protein similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #56 - Aug 2004 Caspases similarity (1) #239 - Nov 2019 Phospholipase A2 similarity (1)

Deposited unit

A: E3 ubiquitin-protein ligase NEDD4

B: E3 ubiquitin-protein ligase NEDD4

hetero molecules

35.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: E3 ubiquitin-protein ligase NEDD4

hetero molecules

defined by author&software
17.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: E3 ubiquitin-protein ligase NEDD4

defined by author&software
17.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	38.778, 47.997, 50.786
Angle α, β, γ (deg.)	108.89, 111.11, 100.86
Int Tables number	1
Space group name H-M	P1

#1: Protein	E3 ubiquitin-protein ligase NEDD4 Mass: 17750.564 Da / Num. of mol.: 2 / Fragment: C2 Domain: Residues 101-252 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4, KIAA0093 / Plasmid: p28a-LIC-TEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P46934, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.23 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% PEG 4000, 0.1 M Succinic acid pH 7.0, 0.01M Spermine tetra-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 11, 2007
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. all: 26613 / Num. obs: 26613 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / R_sym value: 0.046 / Net I/σ(I): 28.51
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 2230 / R_sym value: 0.364 / % possible all: 79.1

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2NSQ

2nsq

Resolution: 1.8→27.23 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.96 / SU B: 5.436 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2086	1357	5.1 %	RANDOM
R_work	0.16852	-	-	-
obs	0.17056	25255	94.78 %	-
all	-	26612	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 30.718 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.24 Å²	-0.4 Å²	0.41 Å²
2-	-	-1.26 Å²	-0.49 Å²
3-	-	-	0.84 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→27.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2330	0	2	221	2553

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	2387
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.456	1.978	3251
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.818	5	290
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.155	23.019	106
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.661	15	395
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.397	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	372
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1811
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	914
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.312	0.2	1591
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	180
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.115	0.2	3
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.242	0.2	55
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.183	0.2	15
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.767	3	1512
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.383	4	2395
X-RAY DIFFRACTION	r_scbond_it	3.418	5	990
X-RAY DIFFRACTION	r_scangle_it	4.852	7	856
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.85 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	90	-
R_work	0.212	1446	-
obs	-	-	72.28 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	9.8663	9.9684	2.7717	20.4287	3.2906	0.8019	-0.2492	0.6049	-0.5439	-0.3118	0.4639	-1.6196	-0.1463	0.398	-0.2147	0.0801	-0.0366	0.0895	0.1308	-0.0174	0.244	-2.2542	27.7556	-2.8359
2	5.4025	-0.4376	0.2412	8.5501	1.3695	43.3586	0.3988	0.3563	0.1665	-0.8965	0.2114	0.1182	-0.4775	-0.7543	-0.6101	0.1357	0.0156	-0.0036	0.0614	0.017	0.0962	-13.3531	28.0867	-3.1284
3	0.9351	1.0609	0.0396	5.8387	2.2891	3.196	0.0377	-0.2672	-0.107	0.886	0.0471	-0.134	0.3676	0.1112	-0.0848	0.2021	0.0374	-0.0314	0.1666	0.0086	0.0772	-10.7567	20.2651	14.5247
4	3.4996	-0.1385	1.0597	6.5794	4.0207	7.4393	0.0154	0.1397	-0.2561	-0.0201	0.1986	-0.2447	0.0737	0.0671	-0.214	0.0458	-0.0026	0.0133	0.0649	0.0109	0.0697	-9.0053	15.7624	2.9736
5	2.2245	0.3305	0.3245	4.2539	1.6107	3.4382	0.0451	-0.1891	-0.0119	0.3541	0.0614	-0.1542	0.1642	0.0185	-0.1064	0.072	0.0109	-0.0044	0.0807	-0.0032	0.0854	-10.6059	21.8579	9.5613
6	12.9042	0.0816	2.9863	7.5482	-0.967	6.2813	0.202	-0.8965	-0.8492	1.1314	-0.1728	-1.123	0.4518	0.3149	-0.0292	0.3471	0.0136	-0.1635	0.1223	0.0969	0.2507	-7.161	12.1311	17.8991
7	3.6411	-2.1778	-1.4473	4.5822	3.8856	4.5436	0.1993	0.1759	0.6615	-0.5897	-0.2213	0.2212	-0.9802	-0.4026	0.022	0.2584	0.1019	-0.0519	0.1903	0.048	0.2512	-19.2723	33.0504	2.0793
8	3.6268	-2.8733	2.3476	24.9577	0.7913	1.8295	0.4072	-0.1308	-0.4783	1.2664	-0.3857	0.8829	0.3	-0.2219	-0.0215	0.1911	-0.0661	0.098	0.1549	0.0166	0.0861	-19.179	15.2103	15.8131
9	2.3319	-1.8065	3.1682	15.9895	1.6664	5.4684	0.0868	-0.3629	-0.1089	1.688	0.0709	0.5851	0.8292	-0.7127	-0.1577	0.3727	-0.0866	0.1154	0.1871	0.0025	0.08	-18.239	18.5446	19.2248
10	10.4952	-3.2425	5.7751	2.4884	3.2263	20.066	0.0129	0.2086	0.0672	-0.2674	-0.121	0.1712	-1.1008	-0.4855	0.1082	0.1864	0.0762	-0.0264	0.0469	0.0005	0.0889	-16.8363	30.8663	-0.1951
11	12.6498	9.4965	1.7568	7.2326	1.7804	2.3061	0.006	0.4334	-0.6624	-0.0974	0.1704	-0.3645	0.4777	0.108	-0.1764	0.1108	-0.0219	0.0213	0.0542	-0.0147	0.2453	14.1823	-10.4262	0.0983
12	17.2343	-9.5009	10.0403	7.1863	-5.4316	11.4676	-0.163	-0.1369	-0.3149	0.416	0.1605	0.1206	0.1368	0.1227	0.0024	0.1125	-0.0108	0.0381	0.0536	0.0532	0.1323	12.9593	-2.8526	8.0085
13	3.0812	0.2353	0.5627	2.6383	-1.1554	3.699	-0.1307	0.3284	0.0402	-0.192	0.0833	0.1774	-0.1767	-0.2322	0.0474	0.0853	0.0015	-0.0076	0.1455	-0.0453	0.1057	0.9739	10.6863	-14.2809
14	12.01	3.0065	6.9774	4.8602	4.3205	7.4143	0.1424	0.2284	-0.421	0.1632	0.056	-0.3	0.1622	0.315	-0.1985	0.0704	-0.0003	0.0282	0.0937	0.006	0.1335	20.4054	4.2644	-1.8591
15	5.2245	-2.5246	1.8869	5.076	-2.7612	5.1495	-0.0609	0.0661	-0.5334	-0.0001	0.1221	0.2059	0.0835	-0.315	-0.0612	0.0344	-0.0339	0.0234	0.0958	-0.0578	0.1396	1.3352	2.6906	-9.7907
16	3.0957	0.5999	0.729	8.1927	-1.8661	2.7442	-0.0381	-0.241	-0.1904	0.3437	-0.0669	-0.303	-0.0205	0.1081	0.105	0.0652	0.0017	0.0165	0.0941	0.0342	0.1551	16.858	2.2044	5.1546
17	1.4384	-1.0131	0.4998	1.9824	1.7887	7.3546	-0.0791	0.1902	0.0108	-0.2544	-0.1239	0.0399	-0.258	-0.0131	0.203	0.1119	-0.0296	0.0048	0.1344	-0.0278	0.1022	9.6935	10.2641	-16.4629
18	2.7788	-1.4807	-0.7216	4.3551	-4.2476	8.0116	-0.2955	-0.3956	-0.1546	0.4173	0.3943	0.4031	0.0225	-0.6839	-0.0987	0.143	0.0088	0.0662	0.237	0.0178	0.1219	8.6094	5.191	9.4763
19	17.7213	7.9317	-10.8236	5.3803	-4.5768	10.3105	-0.0705	-1.1229	-0.2026	0.2563	-0.2288	-0.1127	-0.2378	0.649	0.2993	0.0613	0.0553	0.0131	0.1336	-0.0136	0.0864	4.8054	12.6626	0.2816
20	3.6703	-0.8059	0.7059	1.5564	-0.1022	2.5	0.1227	-0.0082	-0.0433	0.0491	-0.0916	0.134	-0.218	0.1023	-0.0311	0.0619	0.0108	0.0335	0.1041	-0.022	0.0857	6.4024	10.5435	-1.781

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	102 - 114	3 - 15
2	X-RAY DIFFRACTION	2	A	A	115 - 124	16 - 25
3	X-RAY DIFFRACTION	3	A	A	125 - 149	26 - 50
4	X-RAY DIFFRACTION	4	A	A	150 - 164	51 - 65
5	X-RAY DIFFRACTION	5	A	A	165 - 195	66 - 96
6	X-RAY DIFFRACTION	6	A	A	196 - 207	97 - 108
7	X-RAY DIFFRACTION	7	A	A	208 - 225	109 - 126
8	X-RAY DIFFRACTION	8	A	A	226 - 237	127 - 138
9	X-RAY DIFFRACTION	9	A	A	238 - 246	139 - 147
10	X-RAY DIFFRACTION	10	A	A	247 - 252	148 - 153
11	X-RAY DIFFRACTION	11	B	B	102 - 114	3 - 15
12	X-RAY DIFFRACTION	12	B	B	115 - 124	16 - 25
13	X-RAY DIFFRACTION	13	B	B	125 - 144	26 - 45
14	X-RAY DIFFRACTION	14	B	B	145 - 158	46 - 59
15	X-RAY DIFFRACTION	15	B	B	159 - 176	60 - 77
16	X-RAY DIFFRACTION	16	B	B	177 - 188	78 - 89
17	X-RAY DIFFRACTION	17	B	B	189 - 205	90 - 106
18	X-RAY DIFFRACTION	18	B	B	206 - 223	107 - 124
19	X-RAY DIFFRACTION	19	B	B	224 - 234	125 - 135
20	X-RAY DIFFRACTION	20	B	B	235 - 252	136 - 153

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