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- PDB-1ib1: CRYSTAL STRUCTURE OF THE 14-3-3 ZETA:SEROTONIN N-ACETYLTRANSFERAS... -

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Basic information

Entry
Database: PDB / ID: 1ib1
TitleCRYSTAL STRUCTURE OF THE 14-3-3 ZETA:SEROTONIN N-ACETYLTRANSFERASE COMPLEX
Components
  • 14-3-3 ZETA ISOFORM
  • SEROTONIN N-ACETYLTRANSFERASE
KeywordsSIGNALING PROTEIN/TRANSFERASE / N-ACETYL TRANSFERASE / 14-3-3 / SIGNAL TRANSDUCTION / PROTEIN-PROTEIN COMPLEX / PHOSPHORYLATION / SIGNALING PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


aralkylamine N-acetyltransferase / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / N-terminal protein amino acid acetylation / Golgi reassembly / synaptic target recognition / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / tube formation / respiratory system process ...aralkylamine N-acetyltransferase / melatonin biosynthetic process / aralkylamine N-acetyltransferase activity / N-terminal protein amino acid acetylation / Golgi reassembly / synaptic target recognition / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / tube formation / respiratory system process / regulation of synapse maturation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / response to light stimulus / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / cellular response to cAMP / negative regulation of TORC1 signaling / negative regulation of innate immune response / protein sequestering activity / ERK1 and ERK2 cascade / regulation of ERK1 and ERK2 cascade / hippocampal mossy fiber to CA3 synapse / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / lung development / Negative regulation of NOTCH4 signaling / regulation of protein stability / circadian rhythm / protein localization / melanosome / angiogenesis / DNA-binding transcription factor binding / vesicle / blood microparticle / transmembrane transporter binding / cadherin binding / protein phosphorylation / protein domain specific binding / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / RNA binding / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 14-3-3 domain / Delta-Endotoxin; domain 1 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues ...: / 14-3-3 domain / Delta-Endotoxin; domain 1 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COA-S-ACETYL TRYPTAMINE / 14-3-3 protein zeta/delta / Serotonin N-acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsObsil, T. / Ghirlando, R. / Klein, D.C. / Ganguly, S. / Dyda, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Crystal structure of the 14-3-3zeta:serotonin N-acetyltransferase complex. a role for scaffolding in enzyme regulation.
Authors: Obsil, T. / Ghirlando, R. / Klein, D.C. / Ganguly, S. / Dyda, F.
History
DepositionMar 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE SEROTONIN N-ACETYLTRANSFERASE (CHAINS E,F,G,H) WAS EXPRESSED TRUNCATED (ONLY RESIDUES 1-201).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 ZETA ISOFORM
B: 14-3-3 ZETA ISOFORM
C: 14-3-3 ZETA ISOFORM
D: 14-3-3 ZETA ISOFORM
E: SEROTONIN N-ACETYLTRANSFERASE
F: SEROTONIN N-ACETYLTRANSFERASE
G: SEROTONIN N-ACETYLTRANSFERASE
H: SEROTONIN N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,06912
Polymers200,1988
Non-polymers3,8714
Water3,801211
1
A: 14-3-3 ZETA ISOFORM
B: 14-3-3 ZETA ISOFORM
E: SEROTONIN N-ACETYLTRANSFERASE
F: SEROTONIN N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0356
Polymers100,0994
Non-polymers1,9362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-50 kcal/mol
Surface area33370 Å2
MethodPISA
2
C: 14-3-3 ZETA ISOFORM
D: 14-3-3 ZETA ISOFORM
G: SEROTONIN N-ACETYLTRANSFERASE
H: SEROTONIN N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0356
Polymers100,0994
Non-polymers1,9362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-49 kcal/mol
Surface area33620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.717, 75.078, 101.780
Angle α, β, γ (deg.)90.144, 90.063, 63.044
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
14-3-3 ZETA ISOFORM / PROTEIN KINASE C INHIBITOR PROTEIN-1


Mass: 27777.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Plasmid: PET14B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63104
#2: Protein
SEROTONIN N-ACETYLTRANSFERASE / ARALKYLAMINE N-ACETYLTRANSFERASE / AA-NAT / SEROTONIN ACETYLASE


Mass: 22272.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: AANAT OR SNAT / Plasmid: PGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYS
References: UniProt: Q29495, aralkylamine N-acetyltransferase
#3: Chemical
ChemComp-COT / COA-S-ACETYL TRYPTAMINE


Mass: 967.771 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H48N9O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, magnesium chloride, lithium sulfate, DTT, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
220 mMTris-HCl1reservoir
330 %(w/v)PEG40001reservoir
420 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 10, 2000 / Details: TOTAL REFLECTION MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 78001 / Num. obs: 44944 / % possible obs: 84.9 % / Observed criterion σ(I): 0 / Redundancy: 1.74 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 5.6
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.09 / Num. unique all: 3188 / Rsym value: 0.251 / % possible all: 72
Reflection
*PLUS
Num. measured all: 78001
Reflection shell
*PLUS
% possible obs: 72 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4O AND 1CJW

1a4o

1cjw


Resolution: 2.7→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2231 -RANDOM
Rwork0.204 ---
all0.21 44944 --
obs0.204 44626 99.3 %-
Displacement parametersBiso mean: 16.3 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12944 0 252 212 13408
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d1.55
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.034
RfactorNum. reflection% reflection
Rfree0.295 198 -
Rwork0.257 --
obs-3592 72 %

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