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- PDB-5w7j: X-ray structure of the E89A variant of ankyrin repeat domain of D... -

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Basic information

Entry
Database: PDB / ID: 5w7j
TitleX-ray structure of the E89A variant of ankyrin repeat domain of DHHC17 in complex with Snap25b peptide
Components
  • Palmitoyltransferase ZDHHC17
  • Snap25b-111-120
KeywordsPROTEIN BINDING / Palmitoyltransferases / DHHC17 / 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 / Toxicity of botulinum toxin type E (botE) / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / neurotransmitter uptake / Toxicity of botulinum toxin type A (botA) ...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 / Toxicity of botulinum toxin type E (botE) / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / neurotransmitter uptake / Toxicity of botulinum toxin type A (botA) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Acetylcholine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / Serotonin Neurotransmitter Release Cycle / 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 / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / palmitoyltransferase activity / ribbon synapse / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / 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 / myosin binding / Other interleukin signaling / 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 / cell projection / Regulation of insulin secretion / trans-Golgi network / positive regulation of insulin secretion / calcium-dependent protein binding / synaptic vesicle / actin cytoskeleton / lamellipodium / presynaptic membrane / 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: 2.202 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
CitationJournal: 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.
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

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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)55,2594
Polymers55,2594
Non-polymers00
Water1,74797
1
A: Palmitoyltransferase ZDHHC17
B: Snap25b-111-120


Theoretical massNumber of molelcules
Total (without water)27,6302
Polymers27,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-7 kcal/mol
Surface area10790 Å2
MethodPISA
2
C: Palmitoyltransferase ZDHHC17
D: Snap25b-111-120


Theoretical massNumber of molelcules
Total (without water)27,6302
Polymers27,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-7 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.736, 87.736, 128.007
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: 26645.379 Da / Num. of mol.: 2 / Mutation: E89A
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.: 97 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 50 mM Glycine pH 9.0, 18.5% PEG-4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27219 / % possible obs: 97 % / Redundancy: 8 % / Net I/σ(I): 31.1

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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: 2.202→19.86 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.61 / Phase error: 22.78
RfactorNum. reflection% reflection
Rfree0.2111 1323 4.86 %
Rwork0.1701 --
obs0.1721 27208 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.202→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 0 97 3805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073789
X-RAY DIFFRACTIONf_angle_d0.8355161
X-RAY DIFFRACTIONf_dihedral_angle_d8.942641
X-RAY DIFFRACTIONf_chiral_restr0.047591
X-RAY DIFFRACTIONf_plane_restr0.005662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2022-2.29030.2931230.25472477X-RAY DIFFRACTION83
2.2903-2.39440.31971500.23772774X-RAY DIFFRACTION93
2.3944-2.52040.23851630.21322830X-RAY DIFFRACTION96
2.5204-2.67790.26761330.20662949X-RAY DIFFRACTION98
2.6779-2.88410.26361490.20142898X-RAY DIFFRACTION98
2.8841-3.17330.2631490.2032970X-RAY DIFFRACTION99
3.1733-3.630.23871390.183006X-RAY DIFFRACTION100
3.63-4.56430.1791480.14192980X-RAY DIFFRACTION100
4.5643-19.86080.15091690.12763001X-RAY DIFFRACTION100

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