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- PDB-6hj7: The NMR structure of NRADD death domain -

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Basic information

Entry
Database: PDB / ID: 6hj7
TitleThe NMR structure of NRADD death domain
ComponentsDeath domain-containing membrane protein NRADD
KeywordsMEMBRANE PROTEIN / NRAAD / p45 / p75 neurotrophin receptor / bicelles
Function / homology
Function and homology information


death receptor activity / neuron projection membrane / cell body membrane / neurotrophin p75 receptor binding / nerve growth factor binding / nuclear envelope lumen / Rho protein signal transduction / coreceptor activity / lamellipodium / apoptotic process ...death receptor activity / neuron projection membrane / cell body membrane / neurotrophin p75 receptor binding / nerve growth factor binding / nuclear envelope lumen / Rho protein signal transduction / coreceptor activity / lamellipodium / apoptotic process / cell surface / membrane / nucleus / plasma membrane
Similarity search - Function
Tumor necrosis factor receptor member 16, transmembrane domain / : / Tumor necrosis factor receptor member 16 trans-membrane domain / Death Domain, Fas / Death Domain, Fas / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily ...Tumor necrosis factor receptor member 16, transmembrane domain / : / Tumor necrosis factor receptor member 16 trans-membrane domain / Death Domain, Fas / Death Domain, Fas / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Death domain-containing membrane protein NRADD
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsNadezhdin, K.D. / Mineev, K.S. / Goncharuk, S.A. / Arseniev, A.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
14-14-00573 Russian Federation
CitationJournal: Proteins / Year: 2019
Title: NMR structure of a full-length single-pass membrane protein NRADD.
Authors: Nadezhdin, K.D. / Goncharuk, S.A. / Arseniev, A.S. / Mineev, K.S.
History
DepositionSep 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_nmr_spectrometer.model
Revision 2.0Oct 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_seq_id / _chem_comp.formula ..._atom_site.label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.2Jun 19, 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: Death domain-containing membrane protein NRADD


Theoretical massNumber of molelcules
Total (without water)26,6641
Polymers26,6641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8390 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000target function
RepresentativeModel #1target function

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Components

#1: Protein Death domain-containing membrane protein NRADD / Neurotrophin receptor homolog-2 / NRH2 / Neurotrophin receptor-alike death domain protein


Mass: 26664.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nradd / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CJ26

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic13D HN(CO)CA
141isotropic13D HN(CA)CO
151isotropic23D (H)CCH-TOCSY
171isotropic23D 1H-13C NOESY
161isotropic23D 1H-15N NOESY
181isotropic22D 1H-13C HSQC
191isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: bicelle
Contents: 0.2 mM [U-99% 13C; U-99% 15N] NRADD, 8 mM unlabeled DMPC, 8 mM unlabeled CHAPS, 90% H2O/10% D2O
Label: 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMNRADD[U-99% 13C; U-99% 15N]1
8 mMDMPCunlabeled1
8 mMCHAPSunlabeled1
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 6.2 / Pressure: ambient Pa / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 2000 / Conformers submitted total number: 20

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