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- PDB-5w7i: X-ray structure of ankyrin repeat domain of DHHC17 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5w7i
TitleX-ray structure of ankyrin repeat domain of DHHC17 in complex with Snap25b peptide
Components
  • Palmitoyltransferase ZDHHC17
  • Snap25b-111-120
KeywordsPROTEIN BINDING / Palmitoyltransferases / Snap25 / ankyrin repeat domain
Function / homology
Function and homology information


regulation of neurotrophin TRK receptor signaling pathway / protein-cysteine S-myristoyltransferase activity / protein-cysteine S-stearoyltransferase activity / Toxicity of botulinum toxin type C (botC) / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane ...regulation of neurotrophin TRK receptor signaling pathway / protein-cysteine S-myristoyltransferase activity / protein-cysteine S-stearoyltransferase activity / Toxicity of botulinum toxin type C (botC) / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Toxicity of botulinum toxin type A (botA) / Acetylcholine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / palmitoyltransferase activity / ribbon synapse / synaptic vesicle docking / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / regulation of programmed cell death / SNARE complex / SNAP receptor activity / Glutamate Neurotransmitter Release Cycle / Golgi-associated vesicle membrane / neurotransmitter receptor internalization / Sensory processing of sound by inner hair cells of the cochlea / syntaxin-1 binding / SNARE complex assembly / synaptic vesicle priming / lipoprotein transport / regulation of synapse assembly / endosomal transport / Other interleukin signaling / myosin binding / regulation of neuron projection development / exocytosis / synaptic vesicle exocytosis / voltage-gated potassium channel activity / tertiary granule membrane / associative learning / regulation of insulin secretion / long-term memory / specific granule membrane / voltage-gated potassium channel complex / axonal growth cone / presynaptic active zone membrane / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / photoreceptor inner segment / axonogenesis / regulation of ERK1 and ERK2 cascade / locomotory behavior / filopodium / long-term synaptic potentiation / Regulation of insulin secretion / cell projection / trans-Golgi network / positive regulation of insulin secretion / calcium-dependent protein binding / synaptic vesicle / actin cytoskeleton / presynaptic membrane / lamellipodium / cell cortex / growth cone / chemical synaptic transmission / postsynapse / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / cytoskeleton / endosome / neuron projection / protein domain specific binding / Golgi membrane / signaling receptor binding / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / lipid binding / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Palmitoyltransferase, DHHC domain / DHHC palmitoyltransferase / DHHC domain profile. / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Ankyrin repeat-containing domain ...Palmitoyltransferase, DHHC domain / DHHC palmitoyltransferase / DHHC domain profile. / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / 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
Synaptosomal-associated protein 25 / Palmitoyltransferase ZDHHC17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsVerardi, R. / Kim, J.-S. / Ghirlando, R. / Banerjee, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)1ZIAHD008928 United States
Citation
Journal: Structure / Year: 2017
Title: Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase.
Authors: Verardi, R. / Kim, J.S. / Ghirlando, R. / Banerjee, A.
#1: Journal: To Be Published
Title: Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase
Authors: Verardi, R. / Kim, J.-S. / Ghirlando, R. / Banerjee, A.
History
DepositionJun 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Palmitoyltransferase ZDHHC17
B: Snap25b-111-120
C: Palmitoyltransferase ZDHHC17
D: Snap25b-111-120


Theoretical massNumber of molelcules
Total (without water)55,3754
Polymers55,3754
Non-polymers00
Water3,153175
1
A: Palmitoyltransferase ZDHHC17
B: Snap25b-111-120


Theoretical massNumber of molelcules
Total (without water)27,6882
Polymers27,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-6 kcal/mol
Surface area10700 Å2
MethodPISA
2
C: Palmitoyltransferase ZDHHC17
D: Snap25b-111-120


Theoretical massNumber of molelcules
Total (without water)27,6882
Polymers27,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-6 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.187, 88.187, 127.969
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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


Mass: 26703.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZDHHC17, HIP14, HIP3, HYPH, KIAA0946, HSPC294 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IUH5, protein S-acyltransferase
#2: Protein/peptide Snap25b-111-120


Mass: 984.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60880*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl pH 7.5, 12.5% PEG-6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 29948 / % possible obs: 91.8 % / Redundancy: 3.2 % / Net I/σ(I): 17.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EU9

3eu9


Resolution: 2.105→19.92 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 23.91
RfactorNum. reflection% reflection
Rfree0.2222 1547 5.17 %
Rwork0.1759 --
obs0.1783 29948 91.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.105→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 0 175 3878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073776
X-RAY DIFFRACTIONf_angle_d0.8175143
X-RAY DIFFRACTIONf_dihedral_angle_d8.9732225
X-RAY DIFFRACTIONf_chiral_restr0.044590
X-RAY DIFFRACTIONf_plane_restr0.004661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1048-2.17260.35221390.29582245X-RAY DIFFRACTION81
2.1726-2.25020.27371380.27112395X-RAY DIFFRACTION85
2.2502-2.34010.32821300.24742447X-RAY DIFFRACTION88
2.3401-2.44650.28071530.22392534X-RAY DIFFRACTION90
2.4465-2.57520.28051090.20952569X-RAY DIFFRACTION91
2.5752-2.73620.2371380.19192614X-RAY DIFFRACTION93
2.7362-2.94680.25521520.19292643X-RAY DIFFRACTION94
2.9468-3.24220.26451410.18612668X-RAY DIFFRACTION95
3.2422-3.70870.2071540.17062702X-RAY DIFFRACTION96
3.7087-4.66270.17111490.13522767X-RAY DIFFRACTION98
4.6627-19.92110.16251440.13182817X-RAY DIFFRACTION99

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