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- PDB-7bv9: The NMR structure of the BEN domain from human NAC1 -

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Basic information

Entry
Database: PDB / ID: 7bv9
TitleThe NMR structure of the BEN domain from human NAC1
ComponentsNucleus accumbens-associated protein 1
KeywordsNUCLEAR PROTEIN / DNA-binding cancer stem cell
Function / homology
Function and homology information


DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / cell junction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleoplasm ...DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / cell junction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
BEN domain / BEN domain / BEN domain profile. / BEN / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Nucleus accumbens-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsNagata, T. / Kobayashi, N. / Nakayama, N. / Obayashi, E. / Urano, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25893136 Japan
Japan Society for the Promotion of Science (JSPS)17K07307 Japan
Japan Society for the Promotion of Science (JSPS)17H05878 Japan
Japan Society for the Promotion of Science (JSPS)26440026 Japan
Citation
Journal: Biomedicines / Year: 2020
Title: Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner.
Authors: Nakayama, N. / Sakashita, G. / Nagata, T. / Kobayashi, N. / Yoshida, H. / Park, S.Y. / Nariai, Y. / Kato, H. / Obayashi, E. / Nakayama, K. / Kyo, S. / Urano, T.
#1: Journal: Arch. Biochem. Biophys. / Year: 2016
Title: Protein complex formation and intranuclear dynamics of NAC1 in cancer cells.
Authors: Nakayama, N. / Kato, H. / Sakashita, G. / Nariai, Y. / Nakayama, K. / Kyo, S. / Urano, T.
#2: Journal: Carcinogenesis / Year: 2012
Title: Nuclear localization signal in a cancer-related transcriptional regulator protein NAC1.
Authors: Okazaki, K. / Nakayama, N. / Nariai, Y. / Nakayama, K. / Miyazaki, K. / Maruyama, R. / Kato, H. / Kosugi, S. / Urano, T. / Sakashita, G.
#3: Journal: Pathol. Int. / Year: 2012
Title: Low expression of nucleus accumbens-associated protein 1 predicts poor prognosis for patients with pancreatic ductal adenocarcinoma.
Authors: Nishi, T. / Maruyama, R. / Urano, T. / Nakayama, N. / Kawabata, Y. / Yano, S. / Yoshida, M. / Nakayama, K. / Miyazaki, K. / Takenaga, K. / Tanaka, T. / Tajima, Y.
History
DepositionApr 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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

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Assembly

Deposited unit
A: Nucleus accumbens-associated protein 1


Theoretical massNumber of molelcules
Total (without water)18,6371
Polymers18,6371
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nucleus accumbens-associated protein 1 / NAC-1 / BTB/POZ domain-containing protein 14B


Mass: 18637.480 Da / Num. of mol.: 1 / Fragment: BEN domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NACC1, BTBD14B, NAC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: Q96RE7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D CBCA(CO)NH
161isotropic13D HN(CA)CB
171isotropic13D C(CO)NH
181isotropic13D HBHA(CO)NH
191isotropic13D H(CCO)NH
1121isotropic13D CCH-TOCSY
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D (H)CCH-COSY
1141isotropic13D 1H-15N NOESY
1131isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution / Contents: 500 uM [U-13C; U-15N] BEN domain, 95% H2O/5% D2O / Label: 13C_15N_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 500 uM / Component: BEN domain / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 70 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / 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
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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