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Basic information

Entry
Database: PDB / ID: 3jw0
TitleE2~Ubiquitin-HECT
Components
  • E3 ubiquitin-protein ligase NEDD4-like
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE/SIGNALING PROTEIN / Ubiquitin / HECT / E3 / Ubiquitin ligase / UbcH5B / NEDD4L / NEDD4-2 / Ligase / Ubl conjugation pathway / Isopeptide bond / Nucleus / Host-virus interaction / LIGASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


negative regulation of sodium ion import across plasma membrane / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / : / : / protein modification process => GO:0036211 / : ...negative regulation of sodium ion import across plasma membrane / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / : / : / protein modification process => GO:0036211 / : / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization / regulation of sodium ion transmembrane transport / regulation of membrane depolarization / potassium channel inhibitor activity / receptor catabolic process / positive regulation of dendrite extension / (E3-independent) E2 ubiquitin-conjugating enzyme / ventricular cardiac muscle cell action potential / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / E2 ubiquitin-conjugating enzyme / regulation of dendrite morphogenesis / neuromuscular junction development / regulation of synapse organization / ubiquitin conjugating enzyme activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / sodium channel regulator activity / Viral mRNA Translation / protein monoubiquitination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / potassium channel regulator activity / Major pathway of rRNA processing in the nucleolus and cytosol / protein K48-linked ubiquitination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein autoubiquitination / Maturation of protein E / Maturation of protein E / cytosolic ribosome / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / multivesicular body / 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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1
Similarity search - Function
Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / 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, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / 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 / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Protein kinase C conserved region 2 (CalB) / C2 domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / C2 domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin-60S ribosomal protein L40 / E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKamadurai, H.B. / Schulman, B.A.
CitationJournal: Mol.Cell / Year: 2009
Title: Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex.
Authors: Kamadurai, H.B. / Souphron, J. / Scott, D.C. / Duda, D.M. / Miller, D.J. / Stringer, D. / Piper, R.C. / Schulman, B.A.
History
DepositionSep 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin-conjugating enzyme E2 D2
C: E3 ubiquitin-protein ligase NEDD4-like
D: E3 ubiquitin-protein ligase NEDD4-like
X: Ubiquitin
Y: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)141,9676
Polymers141,9676
Non-polymers00
Water34219
1
A: Ubiquitin-conjugating enzyme E2 D2
C: E3 ubiquitin-protein ligase NEDD4-like
X: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)70,9843
Polymers70,9843
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2 D2
D: E3 ubiquitin-protein ligase NEDD4-like
Y: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)70,9843
Polymers70,9843
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.167, 200.571, 109.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsACX / BDY

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin-protein ligase D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2-17 kDa ...Ubiquitin-protein ligase D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / E2(17)KB 2


Mass: 16609.963 Da / Num. of mol.: 2 / Mutation: L3S, C85S, T98K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, UBC4, UBCH5B / Production host: Escherichia coli (E. coli) / References: UniProt: P62837, ubiquitin-protein ligase
#2: Protein E3 ubiquitin-protein ligase NEDD4-like / Nedd4-2 / NEDD4.2


Mass: 45451.637 Da / Num. of mol.: 2 / Fragment: NEDD4L HECT DOMAIN (UNP 576-955) / Mutation: UBIQUITIN G76 ESTER-LINKED TO UBCH5B TO S85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96PU5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Protein Ubiquitin


Mass: 8922.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.38 Å3/Da / Density % sol: 63.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 34028 / Observed criterion σ(F): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.2867 1690 RANDOM
Rwork0.2523 --
all-35274 -
obs-34028 -
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9807 0 0 19 9826

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