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- PDB-5c7j: CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT -

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Basic information

Entry
Database: PDB / ID: 5c7j
TitleCRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT
Components
  • E3 ubiquitin-protein ligase NEDD4
  • Polyubiquitin-C
KeywordsLIGASE/SIGNALING PROTEIN / LIGASE / UBIQUITIN-PROTEIN LIGASE / UBIQUITIN VARIANT / Structural Genomics Consortium / SGC / Structural Genomics / LIGASE-SIGNALING PROTEIN complex
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 / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / regulation of membrane potential / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling
Similarity search - Function
HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWalker, J.R. / Hu, J. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Cell / Year: 2016
Title: System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.
Authors: Zhang, W. / Wu, K.P. / Sartori, M.A. / Kamadurai, H.B. / Ordureau, A. / Jiang, C. / Mercredi, P.Y. / Murchie, R. / Hu, J. / Persaud, A. / Mukherjee, M. / Li, N. / Doye, A. / Walker, J.R. / ...Authors: Zhang, W. / Wu, K.P. / Sartori, M.A. / Kamadurai, H.B. / Ordureau, A. / Jiang, C. / Mercredi, P.Y. / Murchie, R. / Hu, J. / Persaud, A. / Mukherjee, M. / Li, N. / Doye, A. / Walker, J.R. / Sheng, Y. / Hao, Z. / Li, Y. / Brown, K.R. / Lemichez, E. / Chen, J. / Tong, Y. / Harper, J.W. / Moffat, J. / Rotin, D. / Schulman, B.A. / Sidhu, S.S.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation / pdbx_struct_oper_list
Item: _audit_author.name / _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: E3 ubiquitin-protein ligase NEDD4
C: Polyubiquitin-C
D: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)111,8634
Polymers111,8634
Non-polymers00
Water724
1
A: E3 ubiquitin-protein ligase NEDD4
C: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)55,9322
Polymers55,9322
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area23940 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase NEDD4
D: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)55,9322
Polymers55,9322
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-10 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.867, 139.867, 59.386
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLYGLYAA520 - 8952 - 377
21ARGARGGLYGLYBB520 - 8952 - 377
12HISHISLEULEUCC-15 - 733 - 91
22HISHISLEULEUDD-15 - 733 - 91

NCS ensembles :
ID
1
2

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Components

#1: Protein E3 ubiquitin-protein ligase NEDD4 / Cell proliferation-inducing gene 53 protein / Neural precursor cell expressed developmentally down- ...Cell proliferation-inducing gene 53 protein / Neural precursor cell expressed developmentally down-regulated protein 4 / NEDD-4


Mass: 45427.707 Da / Num. of mol.: 2 / Fragment: HECT DOMAIN (UNP RESIDUES 520-900)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4, KIAA0093, NEDD4-1, PIG53 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): V2R
References: UniProt: P46934, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Polyubiquitin-C


Mass: 10503.903 Da / Num. of mol.: 2 / Fragment: UNP residues 1-74 / Mutation: T9A, K11W, T12G, Q62R, K63Y, E64D, T66Q, L71G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): V2R / References: UniProt: P0CG48
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml. The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before ...Details: The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml. The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization. Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04. Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2013 / Details: ADSC Q315
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 26035 / % possible obs: 100 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Χ2: 1.279 / Net I/av σ(I): 34.75 / Net I/σ(I): 8.7 / Num. measured all: 198521
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3-3.057.80.97912860.7540.370.728100
3.05-3.117.80.81113730.8250.3070.7481000.868
3.11-3.177.80.59612750.8880.2260.7591000.638
3.17-3.237.80.53912860.920.2040.7471000.577
3.23-3.37.70.39713120.950.1510.8021000.425
3.3-3.387.80.31712920.9610.120.8011000.339
3.38-3.467.70.23713150.9780.090.8341000.254
3.46-3.567.80.20412460.9850.0770.8411000.218
3.56-3.667.80.16313290.9910.0620.8611000.175
3.66-3.787.80.13213070.9930.050.9441000.142
3.78-3.917.70.09613050.9950.0370.9781000.103
3.91-4.077.70.07712820.9970.0290.9761000.083
4.07-4.267.70.06513250.9980.0250.9841000.069
4.26-4.487.70.06113020.9980.0231.1751000.065
4.48-4.767.60.05512800.9980.0211.2531000.059
4.76-5.137.60.05713020.9980.0221.4871000.061
5.13-5.647.50.06113160.9980.0231.6651000.065
5.64-6.467.40.05612840.9980.0221.6071000.06
6.46-8.137.10.04413160.9990.0181.6671000.048
8.13-506.80.04313020.9970.0186.57699.80.047

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-3000data scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZNV

2znv


Resolution: 3→50.01 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.925 / SU B: 21.55 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27659 549 2.1 %RANDOM
Rwork0.22724 ---
obs0.2283 25473 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.238 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.37 Å20 Å2
2---0.73 Å20 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 3→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7127 0 0 4 7131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197350
X-RAY DIFFRACTIONr_bond_other_d0.0020.026321
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9269992
X-RAY DIFFRACTIONr_angle_other_deg0.9373.00114467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2295914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14524.367371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.784151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7691531
X-RAY DIFFRACTIONr_chiral_restr0.0650.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021800
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_it3.93310.0353671
X-RAY DIFFRACTIONr_mcbond_other3.93310.0363670
X-RAY DIFFRACTIONr_mcangle_it6.24815.0394580
X-RAY DIFFRACTIONr_mcangle_other6.24815.0394581
X-RAY DIFFRACTIONr_scbond_it3.60610.0823679
X-RAY DIFFRACTIONr_scbond_other3.60610.0823680
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.91615.0745413
X-RAY DIFFRACTIONr_long_range_B_refined8.90580.0778434
X-RAY DIFFRACTIONr_long_range_B_other8.90580.0798435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A412800.02
12B412800.02
21C66620.03
22D66620.03
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 43 -
Rwork0.337 1866 -
obs--100 %

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