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- PDB-2ld0: Solution structure of the N-terminal domain of huntingtin (htt17)... -

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Basic information

Entry
Database: PDB / ID: 2ld0
TitleSolution structure of the N-terminal domain of huntingtin (htt17) in 50 % TFE
ComponentsHuntingtin
KeywordsLIPID BINDING PROTEIN / ALPHA HELIX
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 / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / presynaptic cytosol / positive regulation of aggrephagy / postsynaptic cytosol / positive regulation of lipophagy / dynein intermediate chain binding / beta-tubulin binding / Golgi organization / dynactin binding / establishment of mitotic spindle orientation / 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 / dendrite / apoptotic process / 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 / molecular dynamics
Model detailslowest energy, model 1
AuthorsMichalek, M. / Salnikov, E.S. / Werten, S. / Bechinger, B.
CitationJournal: Biophys.J. / Year: 2013
Title: Structure and Topology of the Huntingtin 1-17 Membrane Anchor by a Combined Solution and Solid-State NMR Approach.
Authors: Michalek, M. / Salnikov, E.S. / Bechinger, B.
History
DepositionMay 13, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Huntingtin


Theoretical massNumber of molelcules
Total (without water)1,9751
Polymers1,9751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 1975.417 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-17 / Source method: obtained synthetically / Details: C-terminally amidated peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P42858

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.2 - 0.3 mM 15N labeled at PHE11 htt17, 10 % D2O, 50 % d3 TFE, 40 % PBS, trifluoroethanol/water
Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMhtt17-115N labeled at PHE110.2-0.31
10 %D2O-21
50 %TFE-3d31
40 %PBS-41
Sample conditionsIonic strength: 0.15 / pH: 7.2 / Pressure: ambient / Temperature: 293 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
X-PLOR NIHDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
X-PLOR NIHDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
X-PLOR NIHDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
X-PLOR NIHDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
X-PLOR NIHJohnson, One Moon Scientificprocessing
X-PLOR NIHJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHJohnson, One Moon Scientificdata analysis
X-PLOR NIHJohnson, One Moon Scientificstructure solution
X-PLOR NIHJohnson, One Moon Scientificrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloreprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorechemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloredata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHKoradi, Billeter and Wuthrichprocessing
X-PLOR NIHKoradi, Billeter and Wuthrichchemical shift assignment
X-PLOR NIHKoradi, Billeter and Wuthrichdata analysis
X-PLOR NIHKoradi, Billeter and Wuthrichstructure solution
X-PLOR NIHKoradi, Billeter and Wuthrichrefinement
X-PLOR NIHBhattacharya and Montelioneprocessing
X-PLOR NIHBhattacharya and Montelionechemical shift assignment
X-PLOR NIHBhattacharya and Montelionedata analysis
X-PLOR NIHBhattacharya and Montelionestructure solution
X-PLOR NIHBhattacharya and Montelionerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 109 / NOE intraresidue total count: 36 / NOE long range total count: 0 / NOE medium range total count: 33 / NOE sequential total count: 40
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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