[English] 日本語
Yorodumi
- PDB-6t5f: Human 14-3-3 sigma fused to the StARD1 peptide including phosphos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t5f
TitleHuman 14-3-3 sigma fused to the StARD1 peptide including phosphoserine-195
Components
  • 14-3-3 protein sigma
  • StARD1 peptide
KeywordsSIGNALING PROTEIN / 14-3-3 proteins / Protein chimera / phosphopeptide-binding
Function / homology
Function and homology information


positive regulation of bile acid biosynthetic process / intracellular cholesterol transport / regulation of steroid biosynthetic process / glucocorticoid metabolic process / Pregnenolone biosynthesis / steroid biosynthetic process / cholesterol transfer activity / cholesterol binding / regulation of epidermal cell division / protein kinase C inhibitor activity ...positive regulation of bile acid biosynthetic process / intracellular cholesterol transport / regulation of steroid biosynthetic process / glucocorticoid metabolic process / Pregnenolone biosynthesis / steroid biosynthetic process / cholesterol transfer activity / cholesterol binding / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / 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 / 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 stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / Mitochondrial protein degradation / positive regulation of cell adhesion / cholesterol metabolic process / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / mitochondrial intermembrane space / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / mitochondrial matrix / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Steroidogenic acute regulatory protein / Steroidogenic acute regulatory protein-like / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / START-like domain superfamily / 14-3-3 protein sigma ...Steroidogenic acute regulatory protein / Steroidogenic acute regulatory protein-like / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / START-like domain superfamily / 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
14-3-3 protein sigma / Steroidogenic acute regulatory protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.63 Å
AuthorsSluchanko, N.N. / Tugaeva, K.V. / Titterington, J. / Antson, A.A.
Funding support Russian Federation, United Kingdom, 3items
OrganizationGrant numberCountry
Russian Science Foundation19-74-10031 Russian Federation
Wellcome Trust098230 United Kingdom
Wellcome Trust101528 United Kingdom
CitationJournal: Febs J. / Year: 2020
Title: Molecular basis for the recognition of steroidogenic acute regulatory protein by the 14-3-3 protein family.
Authors: Tugaeva, K.V. / Titterington, J. / Sotnikov, D.V. / Maksimov, E.G. / Antson, A.A. / Sluchanko, N.N.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
E: StARD1 peptide
F: StARD1 peptide
G: StARD1 peptide
H: StARD1 peptide


Theoretical massNumber of molelcules
Total (without water)112,4188
Polymers112,4188
Non-polymers00
Water1,946108
1
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
G: StARD1 peptide
H: StARD1 peptide


Theoretical massNumber of molelcules
Total (without water)56,2094
Polymers56,2094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-17 kcal/mol
Surface area23790 Å2
MethodPISA
2
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
E: StARD1 peptide
F: StARD1 peptide


Theoretical massNumber of molelcules
Total (without water)56,2094
Polymers56,2094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-17 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 74.950, 104.380
Angle α, β, γ (deg.)90.000, 97.980, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 26659.018 Da / Num. of mol.: 4
Fragment: Human 14-3-3 sigma protein is fused to the StARD1 peptide, though not clear which chains connect together in the structure.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide
StARD1 peptide


Mass: 1445.541 Da / Num. of mol.: 4
Fragment: Human 14-3-3 sigma protein is fused to the StARD1 peptide, though not clear which chains connect together in the structure.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P49675*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 20% w/v polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.63→53.51 Å / Num. obs: 35345 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 63.21 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.17 / Net I/σ(I): 5.4
Reflection shellResolution: 2.63→2.72 Å / Redundancy: 4 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3496 / CC1/2: 0.48 / % possible all: 99.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
xia2data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OM0

5om0


Resolution: 2.63→51.69 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.875 / SU R Cruickshank DPI: 0.729 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.675 / SU Rfree Blow DPI: 0.31 / SU Rfree Cruickshank DPI: 0.318
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1811 5.12 %RANDOM
Rwork0.217 ---
obs0.219 35345 99.7 %-
Displacement parametersBiso max: 176.3 Å2 / Biso mean: 80.24 Å2 / Biso min: 23.42 Å2
Baniso -1Baniso -2Baniso -3
1--14.1372 Å20 Å215.9062 Å2
2--17.385 Å20 Å2
3----3.2478 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 2.63→51.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7555 0 0 111 7666
Biso mean---57.09 -
Num. residues----965
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2786SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1312HARMONIC5
X-RAY DIFFRACTIONt_it7658HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion989SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8741SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7658HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10306HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion19.55
LS refinement shellResolution: 2.63→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2707 40 5.66 %
Rwork0.2435 667 -
all0.2453 707 -
obs--88.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.12670.60230.17263.9236-0.882.2008-0.0390.1051-0.03870.0999-0.0531-0.0964-0.0472-0.10010.092-0.19220.0599-0.2215-0.2886-0.10870.251611.9238-18.709440.4305
22.1463-0.99311.20883.67680.51261.56780.1956-0.0315-0.08030.1369-0.1512-0.06860.09070.0208-0.0444-0.1564-0.1103-0.1636-0.26620.05740.12869.852619.232337.9051
31.5681-0.1087-0.13052.2972-0.49921.24760.17010.41120.41050.0466-0.1303-0.0645-0.1728-0.1793-0.03990.06010.1095-0.18620.0330.05360.256656.024138.059115.3425
44.44830.80020.04273.31870.52731.9486-0.05350.2321-0.55410.44110.0590.12230.3862-0.2474-0.00550.0929-0.0589-0.1816-0.0341-0.01340.257245.56931.437118.6809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 233
2X-RAY DIFFRACTION2{ B|* }B0 - 234
3X-RAY DIFFRACTION3{ C|* }C-1 - 233
4X-RAY DIFFRACTION4{ D|* }D1 - 233

+
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