[English] 日本語
Yorodumi
- PDB-5n6n: CRYSTAL STRUCTURE OF THE 14-3-3:NEUTRAL TREHALASE NTH1 COMPLEX -

+
Open data


ID or keywords:

Loading...

-
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 / signal transduction involved in filamentous growth / mitotic spindle orientation checkpoint signaling / alpha,alpha-trehalase / fungal-type cell wall chitin biosynthetic process / cellular response to desiccation / trehalose catabolic process / alpha,alpha-trehalase activity / pseudohyphal growth / ascospore formation ...trehalase activity / signal transduction involved in filamentous growth / mitotic spindle orientation checkpoint signaling / alpha,alpha-trehalase / fungal-type cell wall chitin biosynthetic process / cellular response to desiccation / trehalose catabolic process / alpha,alpha-trehalase activity / pseudohyphal growth / ascospore formation / regulation of glycogen metabolic process / aggresome assembly / negative regulation of ubiquitin protein ligase activity / DNA replication origin binding / enzyme activator activity / phosphoserine residue binding / DNA damage checkpoint signaling / cytoplasmic stress granule / Ras protein signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / 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. / Glycoside hydrolase, family 37 / Trehalase / 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. / Glycoside hydrolase, family 37 / Trehalase / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more