[English] 日本語
Yorodumi
- PDB-6qk8: Crystal structure of yeast 14-3-3 protein (Bmh1) from Saccharomyc... -

+
Open data


ID or keywords:

Loading...

-
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


: / : / signal transduction involved in filamentous growth / mitotic spindle orientation checkpoint signaling / fungal-type cell wall chitin biosynthetic process / pseudohyphal growth / ascospore formation / potassium ion transmembrane transporter activity / regulation of glycogen metabolic process / potassium ion export across plasma membrane ...: / : / signal transduction involved in filamentous growth / mitotic spindle orientation checkpoint signaling / fungal-type cell wall chitin biosynthetic process / pseudohyphal growth / ascospore formation / potassium ion transmembrane transporter activity / regulation of glycogen metabolic process / potassium ion export across plasma membrane / sodium:proton antiporter activity / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / aggresome assembly / negative regulation of ubiquitin protein ligase activity / response to osmotic stress / DNA replication origin binding / enzyme activator activity / sodium ion transmembrane transport / phosphoserine residue binding / DNA damage checkpoint signaling / cytoplasmic stress granule / Ras protein signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / membrane => GO:0016020 / membrane raft / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / 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 / Cation/H+ exchanger / Sodium/hydrogen exchanger family / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...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 / Cation/H+ exchanger / Sodium/hydrogen exchanger family / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
Experiment

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

-
Sample preparation

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

-
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

-
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

+
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