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- PDB-5d2d: Crystal structure of human 14-3-3 zeta in complex with CFTR R-dom... -

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Basic information

Entry
Database: PDB / ID: 5d2d
TitleCrystal structure of human 14-3-3 zeta in complex with CFTR R-domain peptide pS753-pS768
Components
  • 14-3-3 protein zeta/delta
  • Cystic fibrosis transmembrane conductance regulator
KeywordsPEPTIDE BINDING PROTEIN / protein-peptide complex / phosphorylation / tandem binding
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
sucrose / Cystic fibrosis transmembrane conductance regulator / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStevers, L.M. / Leysen, S.F.R. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWO Netherlands
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 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
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 / 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.occupancy / _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.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)56,7179
Polymers55,8903
Non-polymers8266
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-57 kcal/mol
Surface area22450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.862, 112.862, 158.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: HEPES, NaCl, DTT, Li2SO4, Glycine, K2HPO4

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99983 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99983 Å / Relative weight: 1
ReflectionResolution: 1.506→50 Å / Num. obs: 60180 / % possible obs: 99.99 % / Redundancy: 12.3 % / Net I/σ(I): 22.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.085 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 3020 5.02 %
Rwork0.1931 --
obs0.1945 60180 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→48.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 50 196 3976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083909
X-RAY DIFFRACTIONf_angle_d0.965296
X-RAY DIFFRACTIONf_dihedral_angle_d14.3691507
X-RAY DIFFRACTIONf_chiral_restr0.042615
X-RAY DIFFRACTIONf_plane_restr0.004672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13280.31371450.27852528X-RAY DIFFRACTION100
2.1328-2.16780.30771420.26842547X-RAY DIFFRACTION100
2.1678-2.20520.26571060.25422588X-RAY DIFFRACTION100
2.2052-2.24530.29061420.24222533X-RAY DIFFRACTION100
2.2453-2.28850.27091240.23222593X-RAY DIFFRACTION100
2.2885-2.33520.28291530.2232537X-RAY DIFFRACTION100
2.3352-2.38590.25351430.21312558X-RAY DIFFRACTION100
2.3859-2.44140.21351340.22062585X-RAY DIFFRACTION100
2.4414-2.50250.24491550.21212551X-RAY DIFFRACTION100
2.5025-2.57020.2631240.22442580X-RAY DIFFRACTION100
2.5702-2.64580.26931460.22572556X-RAY DIFFRACTION100
2.6458-2.73120.24111300.21782588X-RAY DIFFRACTION100
2.7312-2.82880.25831470.21722575X-RAY DIFFRACTION100
2.8288-2.9420.28561270.22072582X-RAY DIFFRACTION100
2.942-3.07590.24021500.22122599X-RAY DIFFRACTION100
3.0759-3.2380.21911310.21992608X-RAY DIFFRACTION100
3.238-3.44080.20171330.20432592X-RAY DIFFRACTION100
3.4408-3.70640.22341350.18912628X-RAY DIFFRACTION100
3.7064-4.07920.19941220.15812653X-RAY DIFFRACTION100
4.0792-4.66910.18061550.15642640X-RAY DIFFRACTION100
4.6691-5.88090.21121250.17722707X-RAY DIFFRACTION100
5.8809-48.09770.19291510.17632832X-RAY DIFFRACTION100

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