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- PDB-7qi1: Crystal structure of human 14-3-3 protein beta in complex with CF... -

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Basic information

Entry
Database: PDB / ID: 7qi1
TitleCrystal structure of human 14-3-3 protein beta in complex with CFTR peptide pS753pS768 and PPI stabilizer CY007424
Components
  • 14-3-3 protein theta
  • Cystic fibrosis transmembrane conductance regulator
KeywordsPROTEIN TRANSPORT / PPI stabilization / Cystic Fibrosis
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 / negative regulation of monoatomic ion transmembrane transport / 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 / negative regulation of monoatomic ion transmembrane transport / 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 / chloride channel inhibitor activity / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / vesicle docking involved in exocytosis / cholesterol transport / membrane hyperpolarization / bicarbonate transmembrane transporter activity / bicarbonate transport / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / small GTPase-mediated signal transduction / 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 / protein targeting / Activation of BAD and translocation to mitochondria / 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 / chloride transmembrane transport / substantia nigra development / response to endoplasmic reticulum stress / 14-3-3 protein binding / PDZ domain binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / establishment of localization in cell / TP53 Regulates Metabolic Genes / Defective CFTR causes cystic fibrosis / clathrin-coated endocytic vesicle membrane / Late endosomal microautophagy / ABC-family proteins mediated transport / transmembrane transport / recycling endosome / Aggrephagy / Chaperone Mediated Autophagy / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / transmembrane transporter binding / early endosome / endosome membrane / Ub-specific processing proteases / apical plasma membrane / lysosomal membrane / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / synapse / endoplasmic reticulum membrane / enzyme binding / cell surface / signal transduction / ATP hydrolysis activity / protein-containing complex / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
14-3-3 theta / : / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / 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 theta / : / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ARGININE / GLUTAMINE / [2-(2-methylphenyl)sulfanylphenyl]methanamine / TYROSINE / Cystic fibrosis transmembrane conductance regulator / 14-3-3 protein theta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsStevers, L.M. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)024.001.035 Netherlands
CitationJournal: Nat Commun / Year: 2022
Title: Macrocycle-stabilization of its interaction with 14-3-3 increases plasma membrane localization and activity of CFTR.
Authors: Stevers, L.M. / Wolter, M. / Carlile, G.W. / Macdonald, D. / Richard, L. / Gielkens, F. / Hanrahan, J.W. / Thomas, D.Y. / Chakka, S.K. / Peterson, M.L. / Thomas, H. / Brunsveld, L. / Ottmann, C.
History
DepositionDec 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 26, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein theta
B: 14-3-3 protein theta
F: Cystic fibrosis transmembrane conductance regulator
E: Cystic fibrosis transmembrane conductance regulator
C: 14-3-3 protein theta
D: 14-3-3 protein theta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,43914
Polymers114,9766
Non-polymers1,4648
Water9,710539
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14590 Å2
ΔGint-69 kcal/mol
Surface area43320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.367, 111.460, 130.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11F-913-

HOH

21D-391-

HOH

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDFE

#1: Protein
14-3-3 protein theta / 14-3-3 protein T-cell / 14-3-3 protein tau / Protein HS1


Mass: 27115.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: C-terminally truncated 14-3-3 protein beta / Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAQ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27348
#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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13569, EC: 3.6.3.49

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Non-polymers , 5 types, 547 molecules

#3: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2 / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-Q95 / [2-(2-methylphenyl)sulfanylphenyl]methanamine


Mass: 229.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15NS / Source: (synth.) synthetic construct (others) / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / Source: (synth.) synthetic construct (others)
#6: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O3 / Source: (synth.) synthetic construct (others)
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Qiagen Cryos Suite #44 (0.09 M HEPES sodium salt pH7.5, 1.26M tri-sodium citrate, 10% (v/v) glycerol) with an extra 2% (v/v) of glycerol.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.76→56.282 Å / Num. obs: 102027 / % possible obs: 99.87 % / Redundancy: 12.9 % / Biso Wilson estimate: 28.91 Å2 / CC1/2: 1 / Net I/σ(I): 20
Reflection shellResolution: 1.76→1.97 Å / Num. unique obs: 4934 / CC1/2: 0.796

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HEP

6hep


Resolution: 1.76→56.28 Å / SU ML: 0.1978 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4139
Details: A non-canonical order of axes is used in this structure (P2 21 21)
RfactorNum. reflection% reflection
Rfree0.2411 5010 4.91 %
Rwork0.1952 --
obs0.1975 102027 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.9 Å2
Refinement stepCycle: LAST / Resolution: 1.76→56.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7665 0 94 539 8298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617951
X-RAY DIFFRACTIONf_angle_d0.787610740
X-RAY DIFFRACTIONf_chiral_restr0.0431202
X-RAY DIFFRACTIONf_plane_restr0.00461386
X-RAY DIFFRACTIONf_dihedral_angle_d23.24313016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.31041790.24933133X-RAY DIFFRACTION100
1.78-1.80.31081470.2523228X-RAY DIFFRACTION100
1.8-1.820.291840.24363160X-RAY DIFFRACTION99.94
1.82-1.850.24821700.22743200X-RAY DIFFRACTION100
1.85-1.870.24981520.2213207X-RAY DIFFRACTION99.97
1.87-1.90.28471700.22893227X-RAY DIFFRACTION100
1.9-1.920.28681690.24413174X-RAY DIFFRACTION100
1.92-1.950.28641750.23583228X-RAY DIFFRACTION99.97
1.95-1.980.27181420.23363202X-RAY DIFFRACTION100
1.98-2.010.28111770.21373224X-RAY DIFFRACTION100
2.01-2.050.26551710.21673169X-RAY DIFFRACTION100
2.05-2.090.2671550.20823270X-RAY DIFFRACTION100
2.09-2.130.26981760.2073184X-RAY DIFFRACTION100
2.13-2.170.27691500.19913213X-RAY DIFFRACTION99.97
2.17-2.220.27921680.19653226X-RAY DIFFRACTION100
2.22-2.270.23811650.19513250X-RAY DIFFRACTION99.97
2.27-2.330.25311770.20243193X-RAY DIFFRACTION99.94
2.33-2.390.23841680.20013222X-RAY DIFFRACTION99.97
2.39-2.460.24771510.21213240X-RAY DIFFRACTION99.88
2.46-2.540.25461600.20763242X-RAY DIFFRACTION99.77
2.54-2.630.28071800.20643197X-RAY DIFFRACTION99.73
2.63-2.730.25551500.21123246X-RAY DIFFRACTION99.5
2.73-2.860.25981690.20393240X-RAY DIFFRACTION99.68
2.86-3.010.26151830.20833215X-RAY DIFFRACTION99.59
3.01-3.20.24581660.20663273X-RAY DIFFRACTION99.74
3.2-3.440.26071510.19193279X-RAY DIFFRACTION99.74
3.44-3.790.20911600.17913269X-RAY DIFFRACTION99.62
3.79-4.340.22231730.15823299X-RAY DIFFRACTION99.66
4.34-5.470.18661880.16973325X-RAY DIFFRACTION99.94
5.47-56.280.21341840.18423482X-RAY DIFFRACTION99.76

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