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- PDB-1d5f: STRUCTURE OF E6AP: INSIGHTS INTO UBIQUITINATION PATHWAY -

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Basic information

Entry
Database: PDB / ID: 1d5f
TitleSTRUCTURE OF E6AP: INSIGHTS INTO UBIQUITINATION PATHWAY
ComponentsE6AP HECT CATALYTIC DOMAIN, E3 LIGASE
KeywordsLIGASE / BILOBAL STRUCTURE / ELONGATED SHAPE / E3 LIGASE
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 / prostate gland growth / HECT-type E3 ubiquitin transferase / locomotory exploration behavior / androgen receptor signaling pathway / postsynaptic cytosol ...sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / motor learning / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / locomotory exploration behavior / androgen receptor signaling pathway / postsynaptic cytosol / 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 / response to progesterone / positive regulation of protein ubiquitination / response to cocaine / regulation of circadian rhythm / brain development / regulation of synaptic plasticity / response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / rhythmic process / synaptic vesicle / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / proteolysis / zinc ion binding / nucleus / cytosol
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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 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 7, 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 1.3Oct 11, 2017Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.4Jul 18, 2018Group: Data collection / Structure summary / Category: entity / struct
Item: _entity.pdbx_fragment / _struct.pdbx_descriptor / _struct.title
Revision 1.5Feb 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: E6AP HECT CATALYTIC DOMAIN, E3 LIGASE
B: E6AP HECT CATALYTIC DOMAIN, E3 LIGASE
C: E6AP HECT CATALYTIC DOMAIN, E3 LIGASE


Theoretical massNumber of molelcules
Total (without water)124,6213
Polymers124,6213
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-5 kcal/mol
Surface area48280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.5, 113.7, 125.2
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E6AP HECT CATALYTIC DOMAIN, E3 LIGASE


Mass: 41540.434 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q05086, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG1500, AMMONIUM ACETATE,SODIUM CHLORIDE, HEPES-NA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
250 mMHEPES-Na1drop
3200 mM1dropNaCl
45 mMdithiothreitol1drop
511-12 %(w/v)PEG15001reservoir
61.92 Mammonium acetate1reservoir
70.3 M1reservoirNaCl
80.1 MHEPES-Na1reservoir
95 mMdithiothreitol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X4A20.9789
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEMar 28, 1999
ADSC2CCDJun 10, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97891
ReflectionResolution: 2.8→15 Å / Num. all: 127891 / Num. obs: 35446 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 24
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.42 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 127891

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→15 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER (CNS LIBRARY)
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1477 5 %RANDOM
Rwork0.23 ---
all0.251 35446 --
obs0.228 32466 --
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8583 0 0 0 8583
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_deg1.856
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: 2.8 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.012

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