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- PDB-1c4z: STRUCTURE OF AN E6AP-UBCH7 COMPLEX: INSIGHTS INTO THE UBIQUITINAT... -

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Basic information

Entry
Database: PDB / ID: 1c4z
TitleSTRUCTURE OF AN E6AP-UBCH7 COMPLEX: INSIGHTS INTO THE UBIQUITINATION PATHWAY
Components
  • UBIQUITIN CONJUGATING ENZYME E2
  • UBIQUITIN-PROTEIN LIGASE E3A
KeywordsLIGASE / BILOBAL STRUCTURE / ELONGATED SHAPE / E3 UBIQUITIN LIGASE / E2 UBIQUITIN CONJUGATING ENZYME
Function / homology
Function and homology information


sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / motor learning / regulation of ubiquitin-dependent protein catabolic process / cell cycle phase transition / ubiquitin-protein transferase activator activity / prostate gland growth / HECT-type E3 ubiquitin transferase / protein K11-linked ubiquitination ...sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / motor learning / regulation of ubiquitin-dependent protein catabolic process / cell cycle phase transition / ubiquitin-protein transferase activator activity / prostate gland growth / HECT-type E3 ubiquitin transferase / protein K11-linked ubiquitination / cellular response to glucocorticoid stimulus / positive regulation of protein targeting to mitochondrion / positive regulation of ubiquitin-protein transferase activity / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / locomotory exploration behavior / ubiquitin conjugating enzyme activity / androgen receptor signaling pathway / postsynaptic cytosol / ubiquitin ligase complex / protein K48-linked ubiquitination / progesterone receptor signaling pathway / protein autoubiquitination / ovarian follicle development / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of TORC1 signaling / proteasome complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / response to progesterone / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / Regulation of TNFR1 signaling / response to cocaine / regulation of circadian rhythm / brain development / protein modification process / regulation of synaptic plasticity / response to hydrogen peroxide / Regulation of necroptotic cell death / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / rhythmic process / synaptic vesicle / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / ubiquitin protein ligase binding / regulation of DNA-templated transcription / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain superfamily / Amino-terminal Zinc-binding domain of ubiquitin ligase E3A / Ubiquitin-protein ligase E3B/C / Hect, E3 ligase catalytic fold ...Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain superfamily / Amino-terminal Zinc-binding domain of ubiquitin ligase E3A / Ubiquitin-protein ligase E3B/C / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / : / 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 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 L3 / Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsHuang, L. / Kinnucan, E. / Wang, G. / Beaudenon, S. / Howley, P.M. / Huibregtse, J.M. / Pavletich, N.P.
CitationJournal: Science / Year: 1999
Title: Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade.
Authors: Huang, L. / Kinnucan, E. / Wang, G. / Beaudenon, S. / Howley, P.M. / Huibregtse, J.M. / Pavletich, N.P.
History
DepositionOct 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.pdbx_descriptor / _struct.title
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-PROTEIN LIGASE E3A
B: UBIQUITIN-PROTEIN LIGASE E3A
C: UBIQUITIN-PROTEIN LIGASE E3A
D: UBIQUITIN CONJUGATING ENZYME E2


Theoretical massNumber of molelcules
Total (without water)142,5114
Polymers142,5114
Non-polymers00
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.4, 112.7, 123.8
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UBIQUITIN-PROTEIN LIGASE E3A / E6AP


Mass: 41540.434 Da / Num. of mol.: 3 / Fragment: HECT CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX4T-3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q05086, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein UBIQUITIN CONJUGATING ENZYME E2 / UBCH7


Mass: 17889.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P68036, ubiquitin-protein ligase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG1500, MAGNESIUM CHLORIDE, MES-NA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
132 mg/mlprotein1drop
210 %(w/v)PEG15001reservoir
30.2 M1reservoirMgCl2
40.1 Msodium MES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Sep 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 106238 / Num. obs: 42425 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.33 % / Rmerge(I) obs: 0.413 / % possible all: 89.5
Reflection
*PLUS
% possible obs: 89.8 % / Num. measured all: 106238

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→15 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER (CNS LIBRARY)
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1883 -RANDOM 5%
Rwork0.237 ---
all0.262 46056 --
obs0.234 41492 90 %-
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11769 0 0 1077 12846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.707
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.011

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