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- PDB-6tgk: Domain swapped E6AP C-lobe dimer -

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Basic information

Entry
Database: PDB / ID: 6tgk
TitleDomain swapped E6AP C-lobe dimer
ComponentsUbiquitin-protein ligase E3A
KeywordsLIGASE / E6AP / swapped dimer
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 / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of TORC1 signaling / 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
ACETATE ION / Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsRies, L.K. / Feiler, C. / Lowe, L.D. / Liess, A.K.L. / Lorenz, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationLO 2003/1-1 Germany
CitationJournal: Protein Sci. / Year: 2020
Title: Crystal structure of the catalytic C-lobe of the HECT-type ubiquitin ligase E6AP.
Authors: Ries, L.K. / Liess, A.K.L. / Feiler, C.G. / Spratt, D.E. / Lowe, E.D. / Lorenz, S.
History
DepositionNov 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ubiquitin-protein ligase E3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2174
Polymers12,0591
Non-polymers1583
Water1,58588
1
C: Ubiquitin-protein ligase E3A
hetero molecules

C: Ubiquitin-protein ligase E3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4348
Polymers24,1172
Non-polymers3166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z1
Buried area6960 Å2
ΔGint-54 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.280, 72.280, 98.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11C-1038-

HOH

21C-1071-

HOH

31C-1072-

HOH

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Components

#1: Protein 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: 12058.716 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3A, E6AP, EPVE6AP, HPVE6A / Production host: Escherichia coli (E. coli)
References: UniProt: Q05086, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M CaCl 0.1 M Sodiumacetat 30% PEG400

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.3→30.03 Å / Num. obs: 32542 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 17.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01279 / Rpim(I) all: 0.01279 / Rrim(I) all: 0.01809 / Net I/σ(I): 26.56
Reflection shellResolution: 1.3→1.347 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5023 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 3211 / CC1/2: 0.676 / Rpim(I) all: 0.5023 / Rrim(I) all: 0.7103 / % possible all: 99.63

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D5F

1d5f


Resolution: 1.3→30.03 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.991 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED THE CRYSTAL STRUCTURE IS ONLY PARTIALLY DISULFIDE BONDED VIA CYS820 REMARK 3 AND THUS CONTAINS TWO CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 1586 4.9 %RANDOM
Rwork0.178 ---
obs0.1795 30955 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.01 Å2 / Biso mean: 21.552 Å2 / Biso min: 12.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 1.3→30.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms845 0 9 88 942
Biso mean--30.43 31.23 -
Num. residues----105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.013991
X-RAY DIFFRACTIONr_bond_other_d0.0020.017930
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.6681355
X-RAY DIFFRACTIONr_angle_other_deg1.5671.582168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6565130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52321.37958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79215184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.643159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021137
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02226
X-RAY DIFFRACTIONr_rigid_bond_restr5.873971
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 117 -
Rwork0.289 2242 -
all-2359 -
obs--99.54 %
Refinement TLS params.Method: refined / Origin x: 19.8604 Å / Origin y: 5.3654 Å / Origin z: 2.8171 Å
111213212223313233
T0.0146 Å2-0.0149 Å20.0148 Å2-0.0737 Å20.0071 Å2--0.0638 Å2
L0.0431 °20.0167 °20.2131 °2-0.4434 °20.8408 °2--2.375 °2
S-0.004 Å °0.0503 Å °0.0276 Å °-0.0768 Å °0.0814 Å °-0.1177 Å °-0.163 Å °0.346 Å °-0.0774 Å °

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