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- PDB-2lo4: NMR Solution Structure of Optineurin Zinc-finger Domain -

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Basic information

Entry
Database: PDB / ID: 2lo4
TitleNMR Solution Structure of Optineurin Zinc-finger Domain
ComponentsOptineurin
KeywordsPROTEIN TRANSPORT / zinc-finger / nemo
Function / homology
Function and homology information


parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Golgi ribbon formation / negative regulation of receptor recycling / cell death / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling ...parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Golgi ribbon formation / negative regulation of receptor recycling / cell death / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / Golgi organization / autophagosome / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / trans-Golgi network / autophagy / recycling endosome membrane / Regulation of PLK1 Activity at G2/M Transition / protein-macromolecule adaptor activity / defense response to Gram-negative bacterium / Golgi membrane / innate immune response / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWilson, R.C. / Wolfsberger, J. / Twigg, P.D.
CitationJournal: To be Published
Title: NMR Solution Structure of Optineurin Zinc-finger Domain
Authors: Wilson, R.C. / Caudle, T.H. / Wolfsberger, J. / Twigg, P.D.
History
DepositionJan 12, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Optineurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6332
Polymers5,5671
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Optineurin / E3-14.7K-interacting protein / FIP-2 / Huntingtin yeast partner L / Huntingtin-interacting protein ...E3-14.7K-interacting protein / FIP-2 / Huntingtin yeast partner L / Huntingtin-interacting protein 7 / HIP-7 / Huntingtin-interacting protein L / NEMO-related protein / Optic neuropathy-inducing protein / Transcription factor IIIA-interacting protein / TFIIIA-IntP


Mass: 5567.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 / References: UniProt: Q96CV9
#2: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNHA
1613D 1H-15N NOESY
1713D (H)CCH-TOCSY
1822D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] optn550, 50 mM sodium phosphate, 50 mM sodium chloride, 0.12 mM DSS, 90 % H2O, 10 % D2O, 0.9 % sodium azide, 100 uM ZnSO4, 90% H2O/10% D2O90% H2O/10% D2O
21.1 mM [U-100% 15N] optn550, 50 mM sodium phosphate, 50 mM sodium chloride, 0.12 mM DSS, 90 % H2O, 10 % D2O, 0.9 % sodium azide, 100 uM ZnSO4, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMoptn550-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
0.12 mMDSS-41
90 %H2O-51
10 %D2O-61
0.9 %sodium azide-71
100 uMZnSO4-81
1.1 mMoptn550-9[U-100% 15N]2
50 mMsodium phosphate-102
50 mMsodium chloride-112
0.12 mMDSS-122
90 %H2O-132
10 %D2O-142
0.9 %sodium azide-152
100 uMZnSO4-162
Sample conditionspH: 7.3 / Pressure: ambient / Temperature: 273 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
ARIALinge, O'Donoghue and Nilgesrefinement
X-PLORSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLORSchwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: DGSA-distance geometry simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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