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- PDB-6yr6: 14-3-3 sigma in complex with hDM2-186 peptide -

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Basic information

Entry
Database: PDB / ID: 6yr6
Title14-3-3 sigma in complex with hDM2-186 peptide
Components
  • 14-3-3 protein sigma
  • hDM2-186
KeywordsPEPTIDE BINDING PROTEIN / phosphorylated peptide / 1433
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation / Activation of BAD and translocation to mitochondria / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / negative regulation of innate immune response / protein sequestering activity / protein kinase A signaling / protein export from nucleus / positive regulation of cell adhesion / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
IODIDE ION / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsWolter, M. / Srdanovic, S. / Warriner, S. / Wilson, A. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission675179European Union
CitationJournal: Febs J. / Year: 2022
Title: Understanding the interaction of 14-3-3 proteins with hDMX and hDM2: a structural and biophysical study.
Authors: Srdanovic, S. / Wolter, M. / Trinh, C.H. / Ottmann, C. / Warriner, S.L. / Wilson, A.J.
History
DepositionApr 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: hDM2-186
C: 14-3-3 protein sigma
D: hDM2-186
E: 14-3-3 protein sigma
F: hDM2-186
G: 14-3-3 protein sigma
H: hDM2-186
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,63921
Polymers112,6798
Non-polymers1,96113
Water12,484693
1
A: 14-3-3 protein sigma
B: hDM2-186
E: 14-3-3 protein sigma
F: hDM2-186
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,10110
Polymers56,3394
Non-polymers7616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-25 kcal/mol
Surface area22510 Å2
MethodPISA
2
G: 14-3-3 protein sigma
H: hDM2-186
hetero molecules

C: 14-3-3 protein sigma
D: hDM2-186
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,53811
Polymers56,3394
Non-polymers1,1997
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area5000 Å2
ΔGint-21 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.225, 74.569, 77.973
Angle α, β, γ (deg.)98.430, 111.090, 93.120
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 26542.914 Da / Num. of mol.: 4
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
hDM2-186


Mass: 1626.732 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium iodide, 0.1M Bis-Tris propane pH7.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→73.26 Å / Num. obs: 127735 / % possible obs: 97 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.59 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Rrim(I) all: 0.078 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.780.57762540.6810.3650.68595.6
9.59-73.260.057670.9880.0320.05995

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.637
Highest resolutionLowest resolution
Rotation73.26 Å2.12 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
REFMAC5.8.0238refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DAT

4dat


Resolution: 1.75→56.899 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.68
RfactorNum. reflection% reflection
Rfree0.2235 12549 5.02 %
Rwork0.1985 --
obs0.1998 127735 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.12 Å2 / Biso mean: 40.6105 Å2 / Biso min: 17.43 Å2
Refinement stepCycle: final / Resolution: 1.75→56.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7214 0 101 693 8008
Biso mean--52.41 40.74 -
Num. residues----940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047440
X-RAY DIFFRACTIONf_angle_d0.63610040
X-RAY DIFFRACTIONf_chiral_restr0.0341119
X-RAY DIFFRACTIONf_plane_restr0.0031295
X-RAY DIFFRACTIONf_dihedral_angle_d15.2484564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.76990.29223810.2843789794
1.7699-1.79070.29234230.273790094
1.7907-1.81260.28164120.262792295
1.8126-1.83550.28493660.2527776093
1.8355-1.85970.24984450.2376788494
1.8597-1.88510.30174400.2676760893
1.8851-1.91210.33014170.2779792294
1.9121-1.94060.33443780.3012751391
1.9406-1.97090.29084680.2335786594
1.9709-2.00320.22954270.2037778895
2.0032-2.03780.25653560.1987805595
2.0378-2.07480.28194300.2395761592
2.0748-2.11480.22744230.198798295
2.1148-2.15790.21954250.1848783495
2.1579-2.20480.24524400.1854789795
2.2048-2.25610.2234090.2007782193
2.2561-2.31260.22553850.1844797095
2.3126-2.37510.2243630.1762794395
2.3751-2.4450.1974250.1807781094
2.445-2.52390.21244170.1842795695
2.5239-2.61410.21843990.1943794795
2.6141-2.71880.24793950.2043794395
2.7188-2.84250.22494450.197812097
2.8425-2.99240.21174280.2017818997
2.9924-3.17980.2354380.1982801597
3.1798-3.42530.22373940.1938817497
3.4253-3.76990.20744420.1936808097
3.7699-4.31530.18064320.1744810797
4.3153-5.43610.19464590.1737800897
5.4361-56.8990.23214870.2147789095

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