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- PDB-2kr1: Solution NMR structure of zinc binding N-terminal domain of ubiqu... -

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Basic information

Entry
Database: PDB / ID: 2kr1
TitleSolution NMR structure of zinc binding N-terminal domain of ubiquitin-protein ligase E3A from Homo Sapiens. Northeast Structural Genomics Consortium (NESG) target HR3662
ComponentsUbiquitin protein ligase E3A
KeywordsLIGASE / Ubl conjugation pathway / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


positive regulation of macromolecule metabolic process / system development / : / regulation of primary metabolic process / regulation of ubiquitin-dependent protein catabolic process / animal organ development / HECT-type E3 ubiquitin transferase / ligase activity / progesterone receptor signaling pathway / response to progesterone ...positive regulation of macromolecule metabolic process / system development / : / regulation of primary metabolic process / regulation of ubiquitin-dependent protein catabolic process / animal organ development / HECT-type E3 ubiquitin transferase / ligase activity / progesterone receptor signaling pathway / response to progesterone / nuclear receptor-mediated steroid hormone signaling pathway / postsynaptic cytosol / protein autoubiquitination / proteasome complex / negative regulation of TORC1 signaling / protein K48-linked ubiquitination / positive regulation of protein ubiquitination / brain development / regulation of synaptic plasticity / regulation of circadian rhythm / 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 / glutamatergic synapse / proteolysis / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain (AZUL) / GTP Cyclohydrolase I; Chain A, domain 1 / 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) ...Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain (AZUL) / GTP Cyclohydrolase I; Chain A, domain 1 / 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 / Helix non-globular / Special
Similarity search - Domain/homology
Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics
Model detailslowest energy, model 1
AuthorsLemak, A. / Yee, A. / Fares, C. / Semesi, A. / Xiao, R. / Montelione, G. / Dhe-Paganon, S. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG) / Structural Genomics Consortium (SGC)
Citation
Journal: J.Biomol.Nmr / Year: 2011
Title: Zn-binding AZUL domain of human ubiquitin protein ligase Ube3A.
Authors: Lemak, A. / Yee, A. / Bezsonova, I. / Dhe-Paganon, S. / Arrowsmith, C.H.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionNov 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3May 23, 2012Group: Database references
Revision 1.4Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin protein ligase E3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4772
Polymers9,4121
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin protein ligase E3A / CTCL tumor antigen se37-2 / cDNA FLJ77551 / Ubiquitin protein ligase E3A isoform CRA_a / Ubiquitin ...CTCL tumor antigen se37-2 / cDNA FLJ77551 / Ubiquitin protein ligase E3A isoform CRA_a / Ubiquitin protein ligase E3A isoform CRA_b / Human papilloma virus E6-associated protein / Angelman syndrome


Mass: 9411.713 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3A, hCG_18679 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2G0, UniProt: Q05086*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D (H)CCH-TOCSY
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-13C arom NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] hs00184, 10 mM mops, 450 mM sodium chloride, 10 uM ZnSO4, 10 mM DTT, 0.01 % NaN3, 10 mM benzamidine, 10 % D2O-8, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMhs00184-1[U-13C; U-15N]1
10 mMmops-21
450 mMsodium chloride-31
10 uMZnSO4-41
10 mMDTT-51
0.01 %NaN3-61
10 mMbenzamidine-71
10 %D2O-81
Sample conditionsIonic strength: 450 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCLemak, Steren, Llinas, Arrowsmithchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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