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- PDB-8r2o: Huntingtin-Q17, 1-66, N-MBP fusion -

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Basic information

Entry
Database: PDB / ID: 8r2o
TitleHuntingtin-Q17, 1-66, N-MBP fusion
ComponentsMaltodextrin-binding protein,Huntingtin, myristoylated N-terminal fragment
KeywordsUNKNOWN FUNCTION / HUNTINGTIN / HTT-EX1
Function / homology
Function and homology information


positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / positive regulation of mitophagy / regulation of CAMKK-AMPK signaling cascade / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / positive regulation of mitophagy / regulation of CAMKK-AMPK signaling cascade / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / positive regulation of aggrephagy / cell envelope / positive regulation of lipophagy / dynein intermediate chain binding / Golgi organization / beta-tubulin binding / establishment of mitotic spindle orientation / dynactin binding / phosphoprotein phosphatase activity / Regulation of MECP2 expression and activity / postsynaptic cytosol / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / presynaptic cytosol / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / inclusion body / heat shock protein binding / centriole / cytoplasmic vesicle membrane / autophagosome / negative regulation of extrinsic apoptotic signaling pathway / protein destabilization / kinase binding / p53 binding / late endosome / transmembrane transporter binding / periplasmic space / early endosome / positive regulation of apoptotic process / axon / apoptotic process / dendrite / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / protein-containing complex / nucleoplasm / metal ion binding / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / Huntingtin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsToledo-Sherman, L. / Dominguez, C.
Funding support United States, 1items
OrganizationGrant numberCountry
CHDI Foundation United States
CitationJournal: To Be Published
Title: Post-translational modifications in the first 17 amino acids of huntingtin influence self-association and interaction with membranes
Authors: Gallo, M. / Ingenito, R. / Finotto, M. / Di Marino, S. / Cicero, D.O. / Bianchi, E. / Blaesse, M. / Neudegger, T. / Steinbacher, S. / Toledo-Sherman, L. / Lee, M.R. / Dominguez, L. / ...Authors: Gallo, M. / Ingenito, R. / Finotto, M. / Di Marino, S. / Cicero, D.O. / Bianchi, E. / Blaesse, M. / Neudegger, T. / Steinbacher, S. / Toledo-Sherman, L. / Lee, M.R. / Dominguez, L. / Monteagudo, E. / Doherty, E.M.
History
DepositionNov 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein,Huntingtin, myristoylated N-terminal fragment
B: Maltodextrin-binding protein,Huntingtin, myristoylated N-terminal fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8344
Polymers97,1502
Non-polymers6852
Water00
1
A: Maltodextrin-binding protein,Huntingtin, myristoylated N-terminal fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9172
Polymers48,5751
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltodextrin-binding protein,Huntingtin, myristoylated N-terminal fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9172
Polymers48,5751
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)278.619, 278.619, 278.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

#1: Protein Maltodextrin-binding protein,Huntingtin, myristoylated N-terminal fragment


Mass: 48574.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal region of Huntingtin, 1-66, fused to maltose-binding protein,N-terminal region of Huntingtin, 1-66, fused to maltose-binding protein
Source: (gene. exp.) Homo sapiens (human) / Gene: malE, JW3994, HTT, HD, IT15 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LXE0, UniProt: P42858
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.64 Å3/Da / Density % sol: 73.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 0.8 M KH2PO4, 0.8 M NaH2PO4, and 0.1 M TRIS/HCl pH 8.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→47.14 Å / Num. obs: 26757 / % possible obs: 93 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.083 / Net I/σ(I): 12.8
Reflection shellResolution: 3.23→3.48 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5542 / Rrim(I) all: 0.546 / % possible all: 97.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0232refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.23→47.14 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.338 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R: 1.414 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23764 412 1.5 %RANDOM
Rwork0.16649 ---
obs0.16763 26345 93.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.705 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.23→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 46 0 6514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136502
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175858
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.6518873
X-RAY DIFFRACTIONr_angle_other_deg1.2671.57613622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3615831
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76925.517290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90315981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6731510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2875
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027354
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021244
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it25.95412.2663330
X-RAY DIFFRACTIONr_mcbond_other25.95612.2663329
X-RAY DIFFRACTIONr_mcangle_it28.88220.8734159
X-RAY DIFFRACTIONr_mcangle_other28.87820.8744160
X-RAY DIFFRACTIONr_scbond_it31.01413.1653172
X-RAY DIFFRACTIONr_scbond_other31.01313.1643172
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other33.9821.6164714
X-RAY DIFFRACTIONr_long_range_B_refined32.59413.1457300
X-RAY DIFFRACTIONr_long_range_B_other32.59613.1457299
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4823 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.23→3.314 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.536 29 -
Rwork0.461 2022 -
obs--97.85 %

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