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- PDB-6byk: Structure of 14-3-3 beta/alpha bound to O-ClcNAc peptide -

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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


: / 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 / Signaling by Hippo / vacuolar membrane ...: / 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 / Signaling by Hippo / vacuolar membrane / negative regulation of G protein-coupled receptor signaling pathway / Frs2-mediated activation / protein phosphatase inhibitor activity / 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 / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 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 / 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 / nucleus / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.42 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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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