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- PDB-5n6n: CRYSTAL STRUCTURE OF THE 14-3-3:NEUTRAL TREHALASE NTH1 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 5n6n
TitleCRYSTAL STRUCTURE OF THE 14-3-3:NEUTRAL TREHALASE NTH1 COMPLEX
Components
  • Neutral trehalase
  • Protein BMH1
KeywordsSIGNALING PROTEIN / 14-3-3 / neutral trehalase / hydrolase
Function / homology
Function and homology information


trehalase activity / mitotic spindle orientation checkpoint signaling / signal transduction involved in filamentous growth / alpha,alpha-trehalase / alpha,alpha-trehalase activity / cellular response to desiccation / trehalose catabolic process / pseudohyphal growth / chitin biosynthetic process / regulation of glycogen metabolic process ...trehalase activity / mitotic spindle orientation checkpoint signaling / signal transduction involved in filamentous growth / alpha,alpha-trehalase / alpha,alpha-trehalase activity / cellular response to desiccation / trehalose catabolic process / pseudohyphal growth / chitin biosynthetic process / regulation of glycogen metabolic process / ascospore formation / aggresome assembly / DNA replication origin binding / phosphoserine residue binding / negative regulation of protein ubiquitination / DNA damage checkpoint signaling / enzyme activator activity / cytoplasmic stress granule / intracellular protein localization / RNA polymerase II-specific DNA-binding transcription factor binding / Ras protein signal transduction / calcium ion binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / signal transduction / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Neutral trehalase Ca2+ binding / Neutral trehalase Ca2+ binding domain / Trehalase signature 1. / Glycoside hydrolase, family 37, conserved site / Trehalase signature 2. / Trehalase / Glycoside hydrolase, family 37 / 14-3-3 domain / Delta-Endotoxin; domain 1 / Six-hairpin glycosidase-like superfamily ...Neutral trehalase Ca2+ binding / Neutral trehalase Ca2+ binding domain / Trehalase signature 1. / Glycoside hydrolase, family 37, conserved site / Trehalase signature 2. / Trehalase / Glycoside hydrolase, family 37 / 14-3-3 domain / Delta-Endotoxin; domain 1 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
sucrose / Protein BMH1 / Cytosolic neutral trehalase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsAlblova, M. / Smidova, A. / Obsilova, V. / Obsil, T.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular basis of the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1.
Authors: Alblova, M. / Smidova, A. / Docekal, V. / Vesely, J. / Herman, P. / Obsilova, V. / Obsil, T.
History
DepositionFeb 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein BMH1
B: Protein BMH1
C: Neutral trehalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4827
Polymers141,4153
Non-polymers1,0674
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-20 kcal/mol
Surface area46040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.805, 104.749, 105.638
Angle α, β, γ (deg.)90.00, 121.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein BMH1


Mass: 27372.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: BMH1, YER177W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29311
#2: Protein Neutral trehalase / Alpha / alpha-trehalase / alpha-trehalose glucohydrolase


Mass: 86670.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: NTH1, NTH, YDR001C, YD8119.07C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32356, alpha,alpha-trehalase
#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 6.5
Details: 100 mM sodium cacodylate, 200 mM calcium acetate, 18% (w/v) PEG 8000, 12% (w/v) sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2016 / Details: Sagitally bended Si111-crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.29→47.71 Å / Num. obs: 65450 / % possible obs: 97.2 % / Redundancy: 3.5 % / Rsym value: 0.115 / Net I/σ(I): 11.79
Reflection shellResolution: 2.29→2.42 Å / Mean I/σ(I) obs: 1.78 / Num. unique obs: 5711 / Rsym value: 0.679 / % possible all: 85.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTA, homology model of Bmh1 based on 2BR9

5jta

2br9


Resolution: 2.29→46.155 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.02
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 2100 3.21 %Random selection
Rwork0.1844 ---
obs0.1861 65439 97.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.29→46.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9152 0 70 448 9670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089427
X-RAY DIFFRACTIONf_angle_d0.94212793
X-RAY DIFFRACTIONf_dihedral_angle_d20.263449
X-RAY DIFFRACTIONf_chiral_restr0.0511409
X-RAY DIFFRACTIONf_plane_restr0.0051635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2853-2.33850.30331190.27663593X-RAY DIFFRACTION83
2.3385-2.3970.3531310.26823928X-RAY DIFFRACTION91
2.397-2.46180.32071390.25454196X-RAY DIFFRACTION97
2.4618-2.53420.31181420.23214283X-RAY DIFFRACTION99
2.5342-2.6160.27571420.22544291X-RAY DIFFRACTION99
2.616-2.70950.24981420.22054273X-RAY DIFFRACTION99
2.7095-2.81790.31171410.21974276X-RAY DIFFRACTION99
2.8179-2.94620.27551420.24273X-RAY DIFFRACTION99
2.9462-3.10150.25281440.1974333X-RAY DIFFRACTION99
3.1015-3.29570.24281420.19154287X-RAY DIFFRACTION99
3.2957-3.55010.26331420.18484275X-RAY DIFFRACTION98
3.5501-3.90720.21871430.16214307X-RAY DIFFRACTION99
3.9072-4.47220.18631420.14674309X-RAY DIFFRACTION99
4.4722-5.63290.19131440.14754348X-RAY DIFFRACTION99
5.6329-46.16460.18871450.16254367X-RAY DIFFRACTION98

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