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- PDB-3jvz: E2~Ubiquitin-HECT -

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Basic information

Entry
Database: PDB / ID: 3jvz
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 / 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 / negative regulation of sodium ion transmembrane transport / RING-type E3 ubiquitin transferase (cysteine targeting) / 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 / negative regulation of sodium ion transmembrane transport / RING-type E3 ubiquitin transferase (cysteine targeting) / 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 / positive regulation of dendrite extension / (E3-independent) E2 ubiquitin-conjugating enzyme / ventricular cardiac muscle cell action potential / HECT-type E3 ubiquitin transferase / regulation of monoatomic ion transmembrane transport / sodium channel inhibitor activity / E2 ubiquitin-conjugating enzyme / regulation of dendrite morphogenesis / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein monoubiquitination / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / potassium channel regulator activity / 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 / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / cytosolic ribosome / 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 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / multivesicular body / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / regulation of membrane potential / PINK1-PRKN Mediated Mitophagy
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: 3.3 Å
AuthorsSouphron, J. / Kamadurai, 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Structure summary / Category: 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)141,9356
Polymers141,9356
Non-polymers00
Water00
1
A: Ubiquitin-conjugating enzyme E2 D2
C: E3 ubiquitin-protein ligase NEDD4-like
X: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)70,9683
Polymers70,9683
Non-polymers00
Water0
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)70,9683
Polymers70,9683
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.980, 199.888, 109.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 45435.637 Da / Num. of mol.: 2 / Fragment: HECT domain / Mutation: 576-949, C922A
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 / Mutation: Ubiquitin G76 ester linked to UbcH5B S85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS
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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 29147 / Num. obs: 25449 / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 14.55
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.37 / Rsym value: 0.568 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C4O.pdb, 2ONI.pdb

2c4o
PDB Unreleased entry

2oni


Resolution: 3.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1234 -RANDOM
Rwork0.217 ---
obs0.217 25449 87.5 %-
all-29147 --
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9814 0 0 0 9814

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