[English] 日本語
Yorodumi
- PDB-6byk: Structure of 14-3-3 beta/alpha bound to O-ClcNAc peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6byk
TitleStructure of 14-3-3 beta/alpha bound to O-ClcNAc peptide
Components
  • 14-3-3 protein beta/alpha
  • ATPPVSQASSTT O-GlcNac peptide
KeywordsSIGNALING PROTEIN / 14-3-3 / OGT / OGA / O-GlcNac peptide
Function / homology
Function and homology information


: / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / positive regulation of catalytic activity ...: / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / positive regulation of catalytic activity / Signaling by Hippo / vacuolar membrane / negative regulation of G protein-coupled receptor signaling pathway / Frs2-mediated activation / protein kinase inhibitor activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / 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 / RHO GTPases activate PKNs / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / histone deacetylase binding / Negative regulation of MAPK pathway / 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 / Signaling by BRAF and RAF1 fusions / protein localization / melanosome / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / extracellular exosome / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsSchumacher, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2018
Title: Structural basis of O-GlcNAc recognition by mammalian 14-3-3 proteins.
Authors: Toleman, C.A. / Schumacher, M.A. / Yu, S.H. / Zeng, W. / Cox, N.J. / Smith, T.J. / Soderblom, E.J. / Wands, A.M. / Kohler, J.J. / Boyce, M.
History
DepositionDec 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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
G: ATPPVSQASSTT O-GlcNac peptide
J: ATPPVSQASSTT O-GlcNac peptide
K: ATPPVSQASSTT O-GlcNac peptide
R: ATPPVSQASSTT O-GlcNac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,38912
Polymers110,5048
Non-polymers8854
Water00
1
A: 14-3-3 protein beta/alpha
K: ATPPVSQASSTT O-GlcNac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8473
Polymers27,6262
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 14-3-3 protein beta/alpha
G: ATPPVSQASSTT O-GlcNac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8473
Polymers27,6262
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 14-3-3 protein beta/alpha
R: ATPPVSQASSTT O-GlcNac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8473
Polymers27,6262
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 14-3-3 protein beta/alpha
J: ATPPVSQASSTT O-GlcNac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8473
Polymers27,6262
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.670, 71.450, 95.759
Angle α, β, γ (deg.)90.000, 111.610, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 26479.826 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 (E. coli) / References: UniProt: P31946
#2: Protein/peptide
ATPPVSQASSTT O-GlcNac peptide


Mass: 1146.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 4000, 200 mM sodium acetate, 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→89.03 Å / Num. obs: 36435 / % possible obs: 95.7 % / Redundancy: 3 % / Biso Wilson estimate: 65.92 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.063 / Rsym value: 0.087 / Net I/σ(I): 9
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.786 / Rpim(I) all: 0.359 / Rsym value: 0.487 / % possible all: 97.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNK

4dnk


Resolution: 3→89.03 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 30.16
RfactorNum. reflection% reflection
Rfree0.2683 3506 9.62 %
Rwork0.2147 --
obs0.2199 36435 89.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 434.82 Å2 / Biso mean: 86.85 Å2 / Biso min: 11.42 Å2
Refinement stepCycle: final / Resolution: 3→89.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7509 0 56 0 7565
Biso mean--202.22 --
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047678
X-RAY DIFFRACTIONf_angle_d0.72910355
X-RAY DIFFRACTIONf_chiral_restr0.0281169
X-RAY DIFFRACTIONf_plane_restr0.0021335
X-RAY DIFFRACTIONf_dihedral_angle_d15.2912908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.04110.3981260.31611204133082
3.0411-3.08460.33591260.30751290141685
3.0846-3.13060.34321550.29551324147991
3.1306-3.17950.37691730.29921309148290
3.1795-3.23170.32431350.29411373150892
3.2317-3.28740.35831370.29671322145991
3.2874-3.34720.32731360.27011328146489
3.3472-3.41160.35321480.25771347149589
3.4116-3.48120.32081450.27331195134087
3.4812-3.55690.29961320.23851300143286
3.5569-3.63960.33851300.23391277140786
3.6396-3.73070.30421390.22741387152693
3.7307-3.83150.25171500.22331359150993
3.8315-3.94430.26271640.20021324148892
3.9443-4.07160.19131210.19011344146590
4.0716-4.21710.25031480.18931310145888
4.2171-4.3860.23161320.19391264139685
4.386-4.58560.19881250.17471333145888
4.5856-4.82730.25761440.18581354149894
4.8273-5.12970.26411450.1781362150792
5.1297-5.52570.28191360.20771332146891
5.5257-6.08170.24131280.21981277140586
6.0817-6.96140.28141470.21281359150693
6.9614-8.76950.22081440.19761305144988
8.7695-89.06870.20451400.17071350149091
Refinement TLS params.Method: refined / Origin x: -32.6708 Å / Origin y: -16.6755 Å / Origin z: -22.1383 Å
111213212223313233
T0.1514 Å2-0.0096 Å20.0001 Å2-0.1531 Å20.0011 Å2--0.1685 Å2
L-0.114 °20.0134 °2-0.1077 °2-0.2837 °2-0.0424 °2--0.0609 °2
S-0.0015 Å °0.014 Å °0.0237 Å °-0.0451 Å °0.0381 Å °-0.0704 Å °-0.005 Å °-0.0188 Å °0.051 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 232
2X-RAY DIFFRACTION1allB3 - 232
3X-RAY DIFFRACTION1allC3 - 232
4X-RAY DIFFRACTION1allD3 - 232
5X-RAY DIFFRACTION1allG502 - 602
6X-RAY DIFFRACTION1allJ502 - 602
7X-RAY DIFFRACTION1allK503 - 602
8X-RAY DIFFRACTION1allR504 - 602

+
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