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- PDB-6n8c: Structure of the Huntingtin tetramer/dimer mixture determined by ... -

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Basic information

Entry
Database: PDB / ID: 6n8c
TitleStructure of the Huntingtin tetramer/dimer mixture determined by paramagnetic NMR
ComponentsHuntingtin
KeywordsUNKNOWN FUNCTION / tetramer / dimer of dimers
Function / homology
Function and homology information


regulation of cAMP-dependent protein kinase activity / regulation of phosphoprotein phosphatase activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / microtubule-based transport / vocal learning / regulation of CAMKK-AMPK signaling cascade / positive regulation of mitophagy / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly ...regulation of cAMP-dependent protein kinase activity / regulation of phosphoprotein phosphatase activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / microtubule-based transport / vocal learning / regulation of CAMKK-AMPK signaling cascade / positive regulation of mitophagy / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly / presynaptic cytosol / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / positive regulation of aggrephagy / postsynaptic cytosol / positive regulation of lipophagy / dynein intermediate chain binding / beta-tubulin binding / Golgi organization / establishment of mitotic spindle orientation / dynactin binding / Regulation of MECP2 expression and activity / autophagosome / inclusion body / heat shock protein binding / centriole / negative regulation of extrinsic apoptotic signaling pathway / protein destabilization / cytoplasmic vesicle membrane / kinase binding / p53 binding / late endosome / transmembrane transporter binding / early endosome / positive regulation of apoptotic process / axon / apoptotic process / dendrite / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT ...Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSchwieters, C.D. / Kotler, S.A. / Schmidt, T. / Ceccon, A. / Ghirlando, R. / Libich, D.S. / Clore, G.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1FI2GM117609-01 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Probing initial transient oligomerization events facilitating Huntingtin fibril nucleation at atomic resolution by relaxation-based NMR.
Authors: Kotler, S.A. / Tugarinov, V. / Schmidt, T. / Ceccon, A. / Libich, D.S. / Ghirlando, R. / Schwieters, C.D. / Clore, G.M.
History
DepositionNov 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Huntingtin
B: Huntingtin
C: Huntingtin
D: Huntingtin


Theoretical massNumber of molelcules
Total (without water)10,9724
Polymers10,9724
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, sedimentation equilibrium by analytical ultracentrifugation supports the kinetic model observed by NMR
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1100structures with the lowest energy
RepresentativeModel #1best fits pre data

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Components

#1: Protein/peptide
Huntingtin / / Huntington disease protein / HD protein


Mass: 2743.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTT, HD, IT15 / Production host: Escherichia coli (E. coli) / References: UniProt: P42858

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C CT HSQC
232isotropic13D CBCA(CO)NH
242isotropic13D HN(CA)CB
254isotropic23D TOCSY-HSQC
163isotropic113CA SQ CPMG
175isotropic313CA SQ CPMG
183isotropic115N SQ CPMG
195isotropic315N SQ CPMG
2104isotropic11HN PRE
1116isotropic13CA SQ CPMG
1126isotropic15N SQ CPMG

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution21 mM [U-13C; U-15N] httNT-Q7, 90% H2O/10% D2O20 mM sodium phosphate, pH 6.5, 50 mM sodium chlorideU_13C_15N_sample90% H2O/10% D2O
solution40.6 mM [U-15N] httNT-Q7, 90% H2O/10% D2O20 mM sodium phosphate, pH 6.5, 50 mM sodium chloride15N_sample90% H2O/10% D2O
solution31 mM 2-13C glucose; U-15N httNT-Q7, 90% H2O/10% D2O20 mM sodium phosphate, pH 6.5, 50 mM sodium chloride2-13C_15N_sample90% H2O/10% D2O
solution50.75 mM 2-13C glucose; U-15N httNT-Q7, 90% H2O/10% D2O20 mM sodium phosphate, pH 6.5, 50 mM sodium chloride2-13C_15N_sample90% H2O/10% D2O
solution60.4 mM 2-13C glucose; U-15N httNT-Q7, 90% H2O/10% D2O20 mM sodium phosphate, pH 6.5, 50 mM sodium chloride2-13C_15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMhttNT-Q7[U-13C; U-15N]2
0.6 mMhttNT-Q7[U-15N]4
1 mM2-13C glucose, httNT-Q7[U-15N]3
0.75 mM2-13C glucose, httNT-Q7[U-15N]5
0.4 mM2-13C glucose, httNT-Q7[U-15N]6
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mM sodium phosphate, pH 6.5, 50 mM sodium chloride50 mMconditions_16.5 1 atm278 K
220 mM sodium phosphate, pH 6.5, 50 mM sodium chloride50 mMconditions_26.5 1 atm283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE IIIBrukerAVANCE III9003

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.49C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clorestructure calculation
Analysis2.4CCPNchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: utilized rigid backbone coordinates for helix region and employed Xplor-NIH's strict symmetry facility to generage full tetramer from protomer coordinates.
NMR representativeSelection criteria: best fits pre data
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1100 / Conformers submitted total number: 10

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