[English] 日本語
Yorodumi
- PDB-3sml: Crystal structure of human 14-3-3 sigma C38N/N166H in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sml
TitleCrystal structure of human 14-3-3 sigma C38N/N166H in complex with TASK-3 peptide and stabilizer Fusicoccin A aglycone
Components
  • 14-3-3 protein sigma
  • TASK-3 peptide
KeywordsPEPTIDE BINDING PROTEIN / Helical protein / Phosphoprotein / Adapter protein / Nucleus
Function / homology
Function and homology information


negative regulation of aldosterone secretion / regulation of action potential firing rate / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / cellular response to acidic pH / outward rectifier potassium channel activity / regulation of epidermal cell division / protein kinase C inhibitor activity ...negative regulation of aldosterone secretion / regulation of action potential firing rate / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / cellular response to acidic pH / outward rectifier potassium channel activity / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / sodium channel activity / potassium ion import across plasma membrane / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / potassium channel activity / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / visual perception / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / potassium ion transport / intrinsic apoptotic signaling pathway in response to DNA damage / synaptic vesicle / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / mitochondrial inner membrane / regulation of cell cycle / cadherin binding / protein heterodimerization activity / dendrite / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Potassium channel subfamily K member 9 / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / 14-3-3 domain / Delta-Endotoxin; domain 1 / Potassium channel domain / Ion channel / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...Potassium channel subfamily K member 9 / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / 14-3-3 domain / Delta-Endotoxin; domain 1 / Potassium channel domain / Ion channel / 14-3-3 protein sigma / 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
Fusicoccin A aglycone / 14-3-3 protein sigma / Potassium channel subfamily K member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAnders, C. / Schumacher, B. / Ottmann, C.
CitationJournal: Chem. Biol. / Year: 2013
Title: A semisynthetic fusicoccane stabilizes a protein-protein interaction and enhances the expression of K+ channels at the cell surface.
Authors: Anders, C. / Higuchi, Y. / Koschinsky, K. / Bartel, M. / Schumacher, B. / Thiel, P. / Nitta, H. / Preisig-Muller, R. / Schlichthorl, G. / Renigunta, V. / Ohkanda, J. / Daut, J. / Kato, N. / Ottmann, C.
History
DepositionJun 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
P: TASK-3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8478
Polymers27,3062
Non-polymers5416
Water4,252236
1
A: 14-3-3 protein sigma
P: TASK-3 peptide
hetero molecules

A: 14-3-3 protein sigma
P: TASK-3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,69416
Polymers54,6114
Non-polymers1,08212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4980 Å2
ΔGint-71 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.340, 112.050, 62.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-234-

MG

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AP

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26577.920 Da / Num. of mol.: 1 / Mutation: C38N N166H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HME1, SFN / Plasmid: pPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P31947
#2: Protein/peptide TASK-3 peptide


Mass: 727.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NPC2*PLUS

-
Non-polymers , 4 types, 242 molecules

#3: Chemical ChemComp-FW1 / Fusicoccin A aglycone / (2S)-2-[(1S,4R,5R,6R,6aS,9S,9aE,10aR)-1,4,5-trihydroxy-9-(methoxymethyl)-6,10a-dimethyl-1,2,4,5,6,6a,7,8,9,10a-decahydr odicyclopenta[a,d][8]annulen-3-yl]propyl acetate


Mass: 408.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H36O6
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.095M HEPES Na-Salt pH7.4, 25.6% PEG 400, 0.19M CaCl2, 5% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.6 Å / Num. all: 23201 / Num. obs: 23128 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.319 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-20.2218.2512474323999.4
2-2.30.08414.8826327672599.9
2.3-2.50.05721.2711379287099.9
2.5-2.80.04625.1811591290899.9
2.8-30.03929.665441136299.9
3-40.02839.5313713343399.9
4-60.02445.327076180199.8
6-100.02447.43238362999.8
100.02151.3453916183.9

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MAR345softwaredata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3LW1

3lw1


Resolution: 1.9→19.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.464 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 1157 5 %RANDOM
Rwork0.1614 ---
obs0.1636 23127 100 %-
all-21970 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.17 Å2 / Biso mean: 12.3194 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 34 236 2180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222241
X-RAY DIFFRACTIONr_angle_refined_deg1.7642.0053081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8075313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47124.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86815.033461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8051518
X-RAY DIFFRACTIONr_chiral_restr0.1280.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021707
X-RAY DIFFRACTIONr_mcbond_it1.1111.51325
X-RAY DIFFRACTIONr_mcangle_it1.79622172
X-RAY DIFFRACTIONr_scbond_it3.0673916
X-RAY DIFFRACTIONr_scangle_it4.7174.5866
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 84 -
Rwork0.19 1584 -
all-1668 -
obs--100 %

+
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