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- PDB-6qk8: Crystal structure of yeast 14-3-3 protein (Bmh1) from Saccharomyc... -

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Basic information

Entry
Database: PDB / ID: 6qk8
TitleCrystal structure of yeast 14-3-3 protein (Bmh1) from Saccharomyces cerevisiae with the Nha1p (yeast Na+/H+ antiporter) 14-3-3 binding motif Ser481
Components
  • Na(+)/H(+) antiporter
  • Protein BMH1
KeywordsSIGNALING PROTEIN / 14-3-3 protein / Bmh / Na+/H+ antiporter / Nha1p
Function / homology
Function and homology information


mitotic spindle orientation checkpoint signaling / signal transduction involved in filamentous growth / proton export across plasma membrane / pseudohyphal growth / chitin biosynthetic process / regulation of glycogen metabolic process / ascospore formation / potassium ion transmembrane transporter activity / intracellular monoatomic cation homeostasis / potassium ion export across plasma membrane ...mitotic spindle orientation checkpoint signaling / signal transduction involved in filamentous growth / proton export across plasma membrane / pseudohyphal growth / chitin biosynthetic process / regulation of glycogen metabolic process / ascospore formation / potassium ion transmembrane transporter activity / intracellular monoatomic cation homeostasis / potassium ion export across plasma membrane / sodium:proton antiporter activity / sodium ion export across plasma membrane / aggresome assembly / response to osmotic stress / intracellular potassium ion homeostasis / DNA replication origin binding / phosphoserine residue binding / negative regulation of protein ubiquitination / sodium ion transmembrane transport / DNA damage checkpoint signaling / regulation of membrane potential / enzyme activator activity / cytoplasmic stress granule / intracellular protein localization / RNA polymerase II-specific DNA-binding transcription factor binding / Ras protein signal transduction / membrane raft / negative regulation of apoptotic process / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / signal transduction / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Alkali metal cation/H+ antiporter Nha1, C-terminal / Na+/H+ antiporter, budding yeast / Alkali metal cation/H+ antiporter Nha1 C terminus / Na+/H+ antiporter, fungi / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. ...Alkali metal cation/H+ antiporter Nha1, C-terminal / Na+/H+ antiporter, budding yeast / Alkali metal cation/H+ antiporter Nha1 C terminus / Na+/H+ antiporter, fungi / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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
Protein BMH1 / Na(+)/H(+) antiporter
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.917 Å
AuthorsSmidova, A. / Obsil, T. / Obsilova, V.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic17-01953S Czech Republic
CitationJournal: Biochim Biophys Acta Mol Cell Res / Year: 2019
Title: The activity of Saccharomyces cerevisiae Na+, K+/H+antiporter Nha1 is negatively regulated by 14-3-3 protein binding at serine 481.
Authors: Smidova, A. / Stankova, K. / Petrvalska, O. / Lazar, J. / Sychrova, H. / Obsil, T. / Zimmermannova, O. / Obsilova, V.
History
DepositionJan 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Revision 1.2Nov 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: Protein BMH1
D: Protein BMH1
E: Na(+)/H(+) antiporter
F: Na(+)/H(+) antiporter
G: Na(+)/H(+) antiporter
H: Na(+)/H(+) antiporter


Theoretical massNumber of molelcules
Total (without water)111,4688
Polymers111,4688
Non-polymers00
Water00
1
A: Protein BMH1
C: Protein BMH1
E: Na(+)/H(+) antiporter
F: Na(+)/H(+) antiporter


Theoretical massNumber of molelcules
Total (without water)55,7344
Polymers55,7344
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-31 kcal/mol
Surface area21170 Å2
MethodPISA
2
B: Protein BMH1
D: Protein BMH1
G: Na(+)/H(+) antiporter
H: Na(+)/H(+) antiporter


Theoretical massNumber of molelcules
Total (without water)55,7344
Polymers55,7344
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-30 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.850, 59.112, 66.700
Angle α, β, γ (deg.)95.90, 104.14, 91.19
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein BMH1


Mass: 26750.881 Da / Num. of mol.: 4 / Mutation: M237Stop
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BMH1, YER177W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29311
#2: Protein/peptide
Na(+)/H(+) antiporter


Mass: 1116.212 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NHA1, YLR138W, L3149, L9606.4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99271
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

Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7 / Details: KBr, PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 29, 2018 / 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: 2.917→41.141 Å / Num. obs: 16913 / % possible obs: 92.83 % / Redundancy: 2.98 % / Biso Wilson estimate: 43.77 Å2 / CC1/2: 0.986 / Rrim(I) all: 0.167 / Net I/σ(I): 7.23
Reflection shellResolution: 2.917→3.022 Å / Redundancy: 4.81 % / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1720 / CC1/2: 0.723 / Rrim(I) all: 0.617 / % possible all: 94.51

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N6N

5n6n


Resolution: 2.917→41.141 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 846 5 %Random selection
Rwork0.2177 ---
obs0.2204 16906 92.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.917→41.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6883 0 0 0 6883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046997
X-RAY DIFFRACTIONf_angle_d0.5119508
X-RAY DIFFRACTIONf_dihedral_angle_d22.1612444
X-RAY DIFFRACTIONf_chiral_restr0.0331116
X-RAY DIFFRACTIONf_plane_restr0.0031207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9173-3.10010.35851430.29162728X-RAY DIFFRACTION95
3.1001-3.33930.3151460.25782763X-RAY DIFFRACTION95
3.3393-3.67520.29481410.23092684X-RAY DIFFRACTION94
3.6752-4.20650.25411310.19592483X-RAY DIFFRACTION86
4.2065-5.2980.24431450.19472749X-RAY DIFFRACTION96
5.298-41.14460.23561400.19762653X-RAY DIFFRACTION92

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