[English] 日本語
Yorodumi
- PDB-6hep: Crystal structure of human 14-3-3 beta in complex with CFTR R-dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hep
TitleCrystal structure of human 14-3-3 beta in complex with CFTR R-domain peptide pS753-pS768
Components
  • 14-3-3 protein beta/alpha
  • Cystic fibrosis transmembrane conductance regulator
KeywordsSIGNALING PROTEIN / 14-3-3 / CFTR / multivalency
Function / homology
Function and homology information


Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / RHO GTPases regulate CFTR trafficking / transepithelial water transport / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / intracellular pH elevation / amelogenesis ...Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / RHO GTPases regulate CFTR trafficking / transepithelial water transport / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / intracellular pH elevation / amelogenesis / chloride channel inhibitor activity / multicellular organismal-level water homeostasis / water transport / Golgi-associated vesicle membrane / MTOR signalling / chloride channel regulator activity / ARMS-mediated activation / bicarbonate transmembrane transporter activity / membrane hyperpolarization / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / bicarbonate transport / Rap1 signalling / negative regulation of protein import into nucleus / Signaling by Hippo / chloride transmembrane transporter activity / vacuolar membrane / negative regulation of G protein-coupled receptor signaling pathway / Frs2-mediated activation / protein phosphatase inhibitor activity / sperm capacitation / RHOQ GTPase cycle / transcription repressor complex / chloride channel activity / protein kinase inhibitor activity / Regulation of localization of FOXO transcription factors / mTORC1-mediated signalling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / chloride channel complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / 14-3-3 protein binding / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to cAMP / response to endoplasmic reticulum stress / cellular response to forskolin / chloride transmembrane transport / Developmental Lineage of Pancreatic Ductal Cells / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / PDZ domain binding / clathrin-coated endocytic vesicle membrane / phosphoprotein binding / RAF activation / protein sequestering activity / Signaling by high-kinase activity BRAF mutants / Late endosomal microautophagy / MAP2K and MAPK activation / Defective CFTR causes cystic fibrosis / recycling endosome / ABC-family protein mediated transport / intracellular protein localization / recycling endosome membrane / histone deacetylase binding / Chaperone Mediated Autophagy / transmembrane transport / Aggrephagy / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Negative regulation of MAPK pathway / Signaling by BRAF and RAF1 fusions / melanosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / basolateral plasma membrane / early endosome / apical plasma membrane / endosome membrane / Ub-specific processing proteases / cadherin binding / protein domain specific binding / focal adhesion / lysosomal membrane / negative regulation of DNA-templated transcription / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / enzyme binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II
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. ...: / 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
Chem-ETE / Cystic fibrosis transmembrane conductance regulator / 14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 Å
AuthorsStevers, L.M. / Ottmann, C. / Brunsveld, L.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research024.001.035 Netherlands
Netherlands Organisation for Scientific Research2012 022.004.027 Netherlands
Netherlands Organisation for Scientific Research016.150.366 Netherlands
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: A Thermodynamic Model for Multivalency in 14-3-3 Protein-Protein Interactions.
Authors: Stevers, L.M. / de Vink, P.J. / Ottmann, C. / Huskens, J. / Brunsveld, L.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,8808
Polymers114,4636
Non-polymers4172
Water13,241735
1
A: 14-3-3 protein beta/alpha
B: 14-3-3 protein beta/alpha
E: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4404
Polymers57,2323
Non-polymers2081
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-31 kcal/mol
Surface area23340 Å2
MethodPISA
2
C: 14-3-3 protein beta/alpha
D: 14-3-3 protein beta/alpha
F: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4404
Polymers57,2323
Non-polymers2081
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-32 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.619, 111.599, 130.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
14-3-3 protein beta/alpha / Protein 1054 / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26987.451 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31946
#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
#3: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris, 25% v/v PEG350 MME

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.07027 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07027 Å / Relative weight: 1
ReflectionResolution: 1.34→70.62 Å / Num. obs: 231938 / % possible obs: 99.7 % / Redundancy: 12.3 % / Net I/σ(I): 6.7
Reflection shellResolution: 1.68→10 Å

-
Processing

Software
NameVersionClassification
PHENIX(dev_3139: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 1.86→65.375 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.57
RfactorNum. reflection% reflection
Rfree0.251 4375 5.04 %
Rwork0.201 --
obs0.2035 86831 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→65.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7585 0 28 735 8348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077743
X-RAY DIFFRACTIONf_angle_d0.7910421
X-RAY DIFFRACTIONf_dihedral_angle_d6.1326229
X-RAY DIFFRACTIONf_chiral_restr0.0441163
X-RAY DIFFRACTIONf_plane_restr0.0041339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.88110.31151260.28682662X-RAY DIFFRACTION99
1.8811-1.90330.39451380.28822730X-RAY DIFFRACTION99
1.9033-1.92650.32021230.28342715X-RAY DIFFRACTION99
1.9265-1.95090.27441570.27012737X-RAY DIFFRACTION100
1.9509-1.97650.3641470.26272724X-RAY DIFFRACTION100
1.9765-2.00360.31141460.24022749X-RAY DIFFRACTION100
2.0036-2.03230.30271480.23562688X-RAY DIFFRACTION100
2.0323-2.06260.26961400.22372752X-RAY DIFFRACTION99
2.0626-2.09480.27121400.21962694X-RAY DIFFRACTION99
2.0948-2.12920.25511440.21652658X-RAY DIFFRACTION97
2.1292-2.16590.26691540.21782654X-RAY DIFFRACTION97
2.1659-2.20530.25881430.21162742X-RAY DIFFRACTION100
2.2053-2.24770.231460.20882716X-RAY DIFFRACTION100
2.2477-2.29360.27311700.19882753X-RAY DIFFRACTION100
2.2936-2.34340.26611470.19572724X-RAY DIFFRACTION100
2.3434-2.3980.22961470.18872737X-RAY DIFFRACTION100
2.398-2.45790.21641440.18892749X-RAY DIFFRACTION100
2.4579-2.52440.2731430.19042782X-RAY DIFFRACTION100
2.5244-2.59870.27841390.19472746X-RAY DIFFRACTION100
2.5987-2.68260.23521420.20172748X-RAY DIFFRACTION100
2.6826-2.77840.27151820.19732729X-RAY DIFFRACTION100
2.7784-2.88970.26271480.20182738X-RAY DIFFRACTION100
2.8897-3.02120.24011360.20352759X-RAY DIFFRACTION98
3.0212-3.18050.2451500.20122757X-RAY DIFFRACTION99
3.1805-3.37970.22981340.18822824X-RAY DIFFRACTION100
3.3797-3.64070.23011300.19192786X-RAY DIFFRACTION100
3.6407-4.0070.22211440.17862809X-RAY DIFFRACTION100
4.007-4.58670.23131500.16752791X-RAY DIFFRACTION99
4.5867-5.77820.24311420.19072851X-RAY DIFFRACTION99
5.7782-100.22591750.19452952X-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