[English] 日本語
Yorodumi
- PDB-5d3f: Crystal structure of human 14-3-3 zeta in complex with CFTR R-dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d3f
TitleCrystal structure of human 14-3-3 zeta in complex with CFTR R-domain peptide pS753-pS768 and stabilizer fusicoccin-A
Components
  • 14-3-3 protein zeta/delta
  • Cystic fibrosis transmembrane conductance regulator
KeywordsSIGNALING PROTEIN / protein-peptide complex / phosphorylation / tandem binding / stabilization / fusicoccin-A / Structural Genomics / Eindhoven University of Technology
Function / homology
Function and homology information


positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / Golgi reassembly / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation ...positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / Golgi reassembly / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / ATPase-coupled inorganic anion transmembrane transporter activity / amelogenesis / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / chloride channel inhibitor activity / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / establishment of Golgi localization / vesicle docking involved in exocytosis / cholesterol transport / membrane hyperpolarization / bicarbonate transmembrane transporter activity / bicarbonate transport / Rap1 signalling / chloride channel regulator activity / negative regulation of protein localization to nucleus / chloride transmembrane transporter activity / sperm capacitation / KSRP (KHSRP) binds and destabilizes mRNA / chloride channel activity / GP1b-IX-V activation signalling / cholesterol biosynthetic process / RHOQ GTPase cycle / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chloride channel complex / Regulation of localization of FOXO transcription factors / ATPase-coupled transmembrane transporter activity / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / cellular response to glucose starvation / ABC-type transporter activity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / cellular response to forskolin / cellular response to cAMP / RHO GTPases activate PKNs / isomerase activity / negative regulation of TORC1 signaling / chloride transmembrane transport / negative regulation of innate immune response / response to endoplasmic reticulum stress / regulation of ERK1 and ERK2 cascade / protein sequestering activity / PDZ domain binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / establishment of localization in cell / TP53 Regulates Metabolic Genes / Defective CFTR causes cystic fibrosis / clathrin-coated endocytic vesicle membrane / Negative regulation of NOTCH4 signaling / Late endosomal microautophagy / ABC-family proteins mediated transport / transmembrane transport / recycling endosome / Aggrephagy / Chaperone Mediated Autophagy / recycling endosome membrane / melanosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / blood microparticle / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / early endosome / endosome membrane / Ub-specific processing proteases / cadherin binding / apical plasma membrane / lysosomal membrane / protein phosphorylation / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / cell surface / signal transduction / ATP hydrolysis activity / protein-containing complex / extracellular space
Similarity search - Function
: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / 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 ...: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / 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 / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
FUSICOCCIN / Cystic fibrosis transmembrane conductance regulator / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.74 Å
AuthorsStevers, L.M. / Leysen, S.F.R. / Ottmann, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Characterization and small-molecule stabilization of the multisite tandem binding between 14-3-3 and the R domain of CFTR.
Authors: Stevers, L.M. / Lam, C.V. / Leysen, S.F. / Meijer, F.A. / van Scheppingen, D.S. / de Vries, R.M. / Carlile, G.W. / Milroy, L.G. / Thomas, D.Y. / Brunsveld, L. / Ottmann, C.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_struct_assembly_gen ...diffrn_radiation_wavelength / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_struct_assembly_prop.value

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
C: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5714
Polymers55,8903
Non-polymers6811
Water0
1
A: 14-3-3 protein zeta/delta
C: Cystic fibrosis transmembrane conductance regulator

B: 14-3-3 protein zeta/delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5714
Polymers55,8903
Non-polymers6811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4110 Å2
ΔGint-21 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.607, 110.166, 132.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26316.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Protein/peptide Cystic fibrosis transmembrane conductance regulator / / CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP- ...CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP-dependent chloride channel


Mass: 3256.653 Da / Num. of mol.: 1 / Fragment: UNP residues 747-774 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13569, EC: 3.6.3.49
#3: Chemical ChemComp-FSC / FUSICOCCIN / Fusicoccin


Mass: 680.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56O12

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: HEPES, NaCl, DTT, PEG6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97886 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionRedundancy: 5.8 % / Number: 77328 / Rmerge(I) obs: 0.074 / D res high: 2.74 Å / D res low: 44.2 Å / Num. obs: 13354 / % possible obs: 96.9 / Rejects: 21
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.742.8710.3054.7
9.0944.210.0575.2
ReflectionResolution: 2.74→44.2 Å / Num. obs: 13354 / % possible obs: 96.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 60.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Net I/σ(I): 13.7 / Num. measured all: 77328 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.74-2.874.70.3054.1666314080.9440.14878.7
9.09-44.25.20.05723.122004220.9960.02898.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Aimless0.3.11data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→44.011 Å / SU ML: 0.42 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 34.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3026 606 4.56 %
Rwork0.2457 --
obs0.2483 13280 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.74→44.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 48 0 3654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113704
X-RAY DIFFRACTIONf_angle_d1.385015
X-RAY DIFFRACTIONf_dihedral_angle_d15.951367
X-RAY DIFFRACTIONf_chiral_restr0.061579
X-RAY DIFFRACTIONf_plane_restr0.007638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7404-3.01610.40651510.3512804X-RAY DIFFRACTION87
3.0161-3.45240.38131260.31133268X-RAY DIFFRACTION100
3.4524-4.34910.29681590.24743258X-RAY DIFFRACTION100
4.3491-44.01660.26371700.20433344X-RAY DIFFRACTION99

+
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