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- PDB-6byl: Structure of 14-3-3 gamma bound to O-GlcNAcylated thr peptide -

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Basic information

Entry
Database: PDB / ID: 6byl
TitleStructure of 14-3-3 gamma bound to O-GlcNAcylated thr peptide
Components
  • 14-3-3 protein gamma
  • TSASTTVPVTTATTTTTSTW O-GlcNac peptide
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / O-glcNAc
Function / homology
Function and homology information


positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / cellular response to glucose starvation / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / insulin-like growth factor receptor binding / negative regulation of TORC1 signaling / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Transcriptional and post-translational regulation of MITF-M expression and activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein sequestering activity / protein kinase C binding / AURKA Activation by TPX2 / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / receptor tyrosine kinase binding / regulation of synaptic plasticity / positive regulation of T cell activation / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / presynapse / regulation of protein localization / mitochondrial matrix / protein domain specific binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / identical protein binding / nucleus / membrane / cytoplasm / cytosol
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 gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 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 13, 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 gamma
B: 14-3-3 protein gamma
C: 14-3-3 protein gamma
D: 14-3-3 protein gamma
E: 14-3-3 protein gamma
F: 14-3-3 protein gamma
G: TSASTTVPVTTATTTTTSTW O-GlcNac peptide
P: TSASTTVPVTTATTTTTSTW O-GlcNac peptide
T: TSASTTVPVTTATTTTTSTW O-GlcNac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,77112
Polymers172,1079
Non-polymers6643
Water00
1
A: 14-3-3 protein gamma
D: 14-3-3 protein gamma
G: TSASTTVPVTTATTTTTSTW O-GlcNac peptide
P: TSASTTVPVTTATTTTTSTW O-GlcNac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8276
Polymers59,3844
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 14-3-3 protein gamma
C: 14-3-3 protein gamma
T: TSASTTVPVTTATTTTTSTW O-GlcNac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5904
Polymers57,3693
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 14-3-3 protein gamma
F: 14-3-3 protein gamma


Theoretical massNumber of molelcules
Total (without water)55,3542
Polymers55,3542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.200, 121.200, 310.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
14-3-3 protein gamma / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 27676.920 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli (E. coli) / References: UniProt: P61981
#2: Protein/peptide TSASTTVPVTTATTTTTSTW O-GlcNac peptide


Mass: 2015.132 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / 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: 3.32 Å3/Da / Density % sol: 62.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 29% 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 210r / Detector: CCD / Date: Mar 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→112.923 Å / Num. obs: 32119 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 97.7 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.068 / Rrim(I) all: 0.115 / Rsym value: 0.091 / Net I/σ(I): 6.2
Reflection shellResolution: 3.35→3.53 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4440 / CC1/2: 0.53 / Rpim(I) all: 0.613 / Rrim(I) all: 1.003 / Rsym value: 0.785 / % possible all: 91.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata collection
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5USK

5usk
PDB Unreleased entry


Resolution: 3.35→112.923 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2848 1998 6.23 %
Rwork0.2338 --
obs0.237 32075 93.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→112.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11646 0 42 0 11688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311859
X-RAY DIFFRACTIONf_angle_d0.46616017
X-RAY DIFFRACTIONf_dihedral_angle_d13.9824511
X-RAY DIFFRACTIONf_chiral_restr0.021803
X-RAY DIFFRACTIONf_plane_restr0.0022076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3499-3.43370.3941270.35421913X-RAY DIFFRACTION85
3.4337-3.52650.37891430.32792145X-RAY DIFFRACTION96
3.5265-3.63030.34481440.30832169X-RAY DIFFRACTION97
3.6303-3.74750.33991430.28952161X-RAY DIFFRACTION95
3.7475-3.88150.33851390.27972087X-RAY DIFFRACTION93
3.8815-4.03690.28521340.25292034X-RAY DIFFRACTION90
4.0369-4.22060.31751440.25292167X-RAY DIFFRACTION96
4.2206-4.44310.28931450.23992181X-RAY DIFFRACTION96
4.4431-4.72150.28881440.22872169X-RAY DIFFRACTION95
4.7215-5.08610.29711400.22732100X-RAY DIFFRACTION91
5.0861-5.59790.30741470.23962214X-RAY DIFFRACTION97
5.5979-6.40780.28211470.24322208X-RAY DIFFRACTION94
6.4078-8.07290.24681480.21262227X-RAY DIFFRACTION94
8.0729-112.9870.23451530.18092302X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 48.6304 Å / Origin y: -14.4459 Å / Origin z: 15.435 Å
111213212223313233
T0.5416 Å20.0329 Å2-0.0256 Å2-0.4416 Å20.0926 Å2--0.5284 Å2
L0.0305 °20.038 °2-0.089 °2-0.008 °20.1514 °2--0.3032 °2
S0.0238 Å °-0.0432 Å °-0.0182 Å °0.0179 Å °-0.0353 Å °-0.0338 Å °-0.0133 Å °-0.0732 Å °-0 Å °
Refinement TLS groupSelection details: all

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