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- PDB-7qpb: Catalytic C-lobe of the HECT-type ubiquitin ligase E6AP in comple... -

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Basic information

Entry
Database: PDB / ID: 7qpb
TitleCatalytic C-lobe of the HECT-type ubiquitin ligase E6AP in complex with a hybrid foldamer-peptide macrocycle
Components
  • Isoform I of Ubiquitin-protein ligase E3A
  • hybrid foldamer-peptide macrocycle
KeywordsLIGASE / Hect / E3 ligase catalytic domain / ubiquitin protein ligase / transferase activity / catalytic activity
Function / homology
Function and homology information


sperm entry / positive regulation of Golgi lumen acidification / motor learning / negative regulation of dendritic spine morphogenesis / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / progesterone receptor signaling pathway / androgen receptor signaling pathway / locomotory exploration behavior ...sperm entry / positive regulation of Golgi lumen acidification / motor learning / negative regulation of dendritic spine morphogenesis / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / progesterone receptor signaling pathway / androgen receptor signaling pathway / locomotory exploration behavior / protein autoubiquitination / protein K48-linked ubiquitination / ovarian follicle development / negative regulation of TORC1 signaling / cellular response to brain-derived neurotrophic factor stimulus / proteasome complex / response to cocaine / positive regulation of protein ubiquitination / response to progesterone / regulation of synaptic plasticity / response to hydrogen peroxide / regulation of circadian rhythm / brain development / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / rhythmic process / 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 / nucleus / metal ion binding / cytosol
Similarity search - Function
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 domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with
Similarity search - Domain/homology
Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.342 Å
AuthorsDengler, S. / Howard, R.T. / Morozov, V. / Tsiamantas, C. / Douat, C. / Suga, H. / Huc, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HU 1766/2-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Display Selection of a Hybrid Foldamer-Peptide Macrocycle.
Authors: Dengler, S. / Howard, R.T. / Morozov, V. / Tsiamantas, C. / Huang, W.E. / Liu, Z. / Dobrzanski, C. / Pophristic, V. / Brameyer, S. / Douat, C. / Suga, H. / Huc, I.
History
DepositionJan 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _citation.journal_volume / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_torsion / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.type / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform I of Ubiquitin-protein ligase E3A
B: Isoform I of Ubiquitin-protein ligase E3A
C: Isoform I of Ubiquitin-protein ligase E3A
D: Isoform I of Ubiquitin-protein ligase E3A
H: hybrid foldamer-peptide macrocycle
I: hybrid foldamer-peptide macrocycle


Theoretical massNumber of molelcules
Total (without water)56,1146
Polymers56,1146
Non-polymers00
Water1,02757
1
C: Isoform I of Ubiquitin-protein ligase E3A
H: hybrid foldamer-peptide macrocycle

A: Isoform I of Ubiquitin-protein ligase E3A


  • defined by author&software
  • Evidence: native gel electrophoresis, In the absence of the reducing agent, the protein undergoes spontenous oxidation forming a dimer thrhough an intermolecular Cys820-Cys820 disulfide bond. The ...Evidence: native gel electrophoresis, In the absence of the reducing agent, the protein undergoes spontenous oxidation forming a dimer thrhough an intermolecular Cys820-Cys820 disulfide bond. The formation of the disulfide bond-mediated dimer in solution can be confirmed by non-reducing native gel electrophoresis.
  • 28.1 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)28,0573
Polymers28,0573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1610 Å2
ΔGint-13 kcal/mol
Surface area11960 Å2
MethodPISA
2
A: Isoform I of Ubiquitin-protein ligase E3A
C: Isoform I of Ubiquitin-protein ligase E3A
H: hybrid foldamer-peptide macrocycle

A: Isoform I of Ubiquitin-protein ligase E3A
C: Isoform I of Ubiquitin-protein ligase E3A
H: hybrid foldamer-peptide macrocycle


  • defined by author&software
  • Evidence: native gel electrophoresis, In the absence of the reducing agent, the protein undergoes spontenous oxidation forming a dimer thrhough an intermolecular Cys820-Cys820 disulfide bond. The ...Evidence: native gel electrophoresis, In the absence of the reducing agent, the protein undergoes spontenous oxidation forming a dimer thrhough an intermolecular Cys820-Cys820 disulfide bond. The formation of the disulfide bond-mediated dimer in solution can be confirmed by non-reducing native gel electrophoresis.
  • 56.1 kDa, 6 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)56,1146
Polymers56,1146
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5290 Å2
ΔGint-36 kcal/mol
Surface area21870 Å2
MethodPISA
3
D: Isoform I of Ubiquitin-protein ligase E3A
I: hybrid foldamer-peptide macrocycle

B: Isoform I of Ubiquitin-protein ligase E3A


Theoretical massNumber of molelcules
Total (without water)28,0573
Polymers28,0573
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1580 Å2
ΔGint-12 kcal/mol
Surface area12150 Å2
MethodPISA
4
B: Isoform I of Ubiquitin-protein ligase E3A
D: Isoform I of Ubiquitin-protein ligase E3A
I: hybrid foldamer-peptide macrocycle

B: Isoform I of Ubiquitin-protein ligase E3A
D: Isoform I of Ubiquitin-protein ligase E3A
I: hybrid foldamer-peptide macrocycle


Theoretical massNumber of molelcules
Total (without water)56,1146
Polymers56,1146
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5290 Å2
ΔGint-36 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.910, 59.050, 67.300
Angle α, β, γ (deg.)90.00, 95.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Isoform I of Ubiquitin-protein ligase E3A / E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6- ...E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6-associated protein / Oncogenic protein-associated protein E6-AP / Renal carcinoma antigen NY-REN-54


Mass: 12961.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3A, E6AP, EPVE6AP, HPVE6A / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q05086, HECT-type E3 ubiquitin transferase
#2: Protein/peptide hybrid foldamer-peptide macrocycle


Mass: 2133.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% PEG 8000, 0.1 M sodium cacodylate, 0.1 M calcium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.342→29.53 Å / Num. obs: 24491 / % possible obs: 98.35 % / Redundancy: 3.5 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.06614 / Rpim(I) all: 0.04175 / Rrim(I) all: 0.07841 / Net I/σ(I): 11.91
Reflection shellResolution: 2.342→2.426 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.6111 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 2402 / CC1/2: 0.669 / CC star: 0.895 / Rpim(I) all: 0.3868 / Rrim(I) all: 0.7249 / % possible all: 97.05

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C4Z

1c4z


Resolution: 2.342→29.53 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2626 1225 5 %
Rwork0.2149 --
obs0.2173 24488 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.342→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 306 57 3744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023786
X-RAY DIFFRACTIONf_angle_d0.625123
X-RAY DIFFRACTIONf_dihedral_angle_d18.807563
X-RAY DIFFRACTIONf_chiral_restr0.035549
X-RAY DIFFRACTIONf_plane_restr0.003645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.342-2.440.32741330.28142526X-RAY DIFFRACTION97
2.44-2.550.33481360.27592592X-RAY DIFFRACTION99
2.55-2.680.32951370.27392595X-RAY DIFFRACTION99
2.68-2.850.3631350.26932571X-RAY DIFFRACTION99
2.85-3.070.31451380.25112615X-RAY DIFFRACTION99
3.07-3.380.27641340.23512555X-RAY DIFFRACTION98
3.38-3.860.2671380.20372604X-RAY DIFFRACTION99
3.86-4.860.22441360.18562594X-RAY DIFFRACTION98
4.87-29.530.21991380.18632611X-RAY DIFFRACTION96

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