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- PDB-3eu9: The ankyrin repeat domain of Huntingtin interacting protein 14 -

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Basic information

Entry
Database: PDB / ID: 3eu9
TitleThe ankyrin repeat domain of Huntingtin interacting protein 14
ComponentsHuntingtin-interacting protein 14
Keywordsprotein binding / methyl-lysine-binding protein / epigenetics / ankyrin repeats / methyllyine binding / Huntingtin interacting protein 14 / Acyltransferase / ANK repeat / Cytoplasmic vesicle / Golgi apparatus / Membrane / Metal-binding / Oncogene / Phosphoprotein / Transferase / Transmembrane / Zinc-finger
Function / homology
Function and homology information


regulation of neurotrophin TRK receptor signaling pathway / protein-cysteine S-myristoyltransferase activity / protein-cysteine S-stearoyltransferase activity / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / regulation of programmed cell death / Golgi-associated vesicle membrane / lipoprotein transport ...regulation of neurotrophin TRK receptor signaling pathway / protein-cysteine S-myristoyltransferase activity / protein-cysteine S-stearoyltransferase activity / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / regulation of programmed cell death / Golgi-associated vesicle membrane / lipoprotein transport / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / axonogenesis / regulation of ERK1 and ERK2 cascade / cell projection / presynaptic membrane / positive regulation of canonical NF-kappaB signal transduction / Golgi membrane / intracellular membrane-bounded organelle / signaling receptor binding / Golgi apparatus / identical protein binding
Similarity search - Function
Palmitoyltransferase, DHHC domain / DHHC palmitoyltransferase / DHHC domain profile. / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Palmitoyltransferase, DHHC domain / DHHC palmitoyltransferase / DHHC domain profile. / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
HISTIDINE / Palmitoyltransferase ZDHHC17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å
AuthorsGao, T. / Collins, R.E. / Horton, J.R. / Zhang, R. / Zhang, X. / Cheng, X.
CitationJournal: Proteins / Year: 2009
Title: The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding.
Authors: Gao, T. / Collins, R.E. / Horton, J.R. / Zhang, X. / Zhang, R. / Dhayalan, A. / Tamas, R. / Jeltsch, A. / Cheng, X.
History
DepositionOct 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Huntingtin-interacting protein 14
B: Huntingtin-interacting protein 14
C: Huntingtin-interacting protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,62113
Polymers80,6083
Non-polymers1,01310
Water6,161342
1
A: Huntingtin-interacting protein 14
B: Huntingtin-interacting protein 14
C: Huntingtin-interacting protein 14
hetero molecules

A: Huntingtin-interacting protein 14
B: Huntingtin-interacting protein 14
C: Huntingtin-interacting protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,24226
Polymers161,2176
Non-polymers2,02620
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area15010 Å2
ΔGint-224 kcal/mol
Surface area51010 Å2
MethodPISA
2
A: Huntingtin-interacting protein 14
C: Huntingtin-interacting protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,56010
Polymers53,7392
Non-polymers8218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-73 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.660, 106.660, 255.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

DetailsThe crystallographic asymmetric unit contains three monomer molecules.

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Components

#1: Protein Huntingtin-interacting protein 14 / Hip14 / Palmitoyltransferase ZDHHC17 / Zinc finger DHHC domain-containing protein 17 / DHHC-17 / ...Hip14 / Palmitoyltransferase ZDHHC17 / Zinc finger DHHC domain-containing protein 17 / DHHC-17 / Huntingtin-interacting protein 3 / Huntingtin-interacting protein H / Huntingtin yeast partner H / Putative NF-kappa-B-activating protein 205 / Putative MAPK-activating protein PM11


Mass: 26869.482 Da / Num. of mol.: 3 / Fragment: ankyrin repeats
Source method: isolated from a genetically manipulated source
Details: The gene fragment encoding the N-terminal 51-288 residues of HIP14 was amplified from ATCC Clone 5266097 and cloned into the NdeI and XhoI restriction sites of a modified pET28b vector ...Details: The gene fragment encoding the N-terminal 51-288 residues of HIP14 was amplified from ATCC Clone 5266097 and cloned into the NdeI and XhoI restriction sites of a modified pET28b vector containing 6xHis tag followed by SUMO tag, yielding pXC650.
Source: (gene. exp.) Homo sapiens (human) / Gene: ZDHHC17, HIP14, HIP3, HYPH, KIAA0946, HSPC294 / Plasmid: pXC650 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IUH5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 289 K / pH: 5.5
Details: 100 mM (NH4)2SO4, 25% polyethylene glycol (PEG) 3350, 0.1M Bis-Tris, pH 5.5. , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9796, 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97941
ReflectionResolution: 1.99→35 Å / Num. obs: 59687 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14
Reflection shellResolution: 1.99→2.05 Å / Rmerge(I) obs: 0.404 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.99→34.27 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 553241.64 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL ANISOTROPIC B VALUE / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2937 4.9 %RANDOM
Rwork0.222 ---
obs0.222 58266 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.8752 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 40.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.197 Å20 Å20 Å2
2--0.197 Å20 Å2
3----0.395 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-34.3 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.99→34.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 57 342 5611
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.9281.5
X-RAY DIFFRACTIONc_mcangle_it1.5212
X-RAY DIFFRACTIONc_scbond_it1.3492
X-RAY DIFFRACTIONc_scangle_it2.0192.5
LS refinement shellResolution: 1.99→2.06 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.289 275 5.2 %
Rwork0.269 4980 -
obs--89.5 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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