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- PDB-6yr7: 14-3-3 sigma in complex with hDMX-342+367 peptide -

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Basic information

Entry
Database: PDB / ID: 6yr7
Title14-3-3 sigma in complex with hDMX-342+367 peptide
Components
  • 14-3-3 protein sigma
  • Protein Mdm4
KeywordsPEPTIDE BINDING PROTEIN / bivalent binding mode / 1433
Function / homology
Function and homology information


atrial septum development / ventricular septum development / atrioventricular valve morphogenesis / heart valve development / endocardial cushion morphogenesis / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / transcription repressor complex / regulation of cell-cell adhesion ...atrial septum development / ventricular septum development / atrioventricular valve morphogenesis / heart valve development / endocardial cushion morphogenesis / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / transcription repressor complex / regulation of cell-cell adhesion / negative regulation of signal transduction by p53 class mediator / establishment of skin barrier / Regulation of localization of FOXO transcription factors / Regulation of GBP-mediated host defense / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of protein localization to plasma membrane / cAMP/PKA signal transduction / protein export from nucleus / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / release of cytochrome c from mitochondria / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of protein localization / positive regulation of protein export from nucleus / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / DNA damage response, signal transduction by p53 class mediator / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / negative regulation of protein catabolic process / Stabilization of p53 / protein sequestering activity / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / intracellular protein localization / enzyme activator activity / Regulation of TP53 Degradation / regulation of protein localization / positive regulation of cell growth / protein-containing complex assembly / cellular response to hypoxia / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / protein stabilization / Ub-specific processing proteases / cadherin binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / : / extracellular exosome / nucleoplasm / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MDM4 / : / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / 14-3-3 domain / Zn-finger in Ran binding protein and others / Delta-Endotoxin; domain 1 / Zinc finger, C3HC4 type (RING finger) ...MDM4 / : / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / 14-3-3 domain / Zn-finger in Ran binding protein and others / Delta-Endotoxin; domain 1 / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein Mdm4 / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
Q: Protein Mdm4
C: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4285
Polymers62,1464
Non-polymers2821
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-22 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.106, 70.213, 80.626
Angle α, β, γ (deg.)90.000, 101.970, 90.000
Int Tables number5
Space group name H-MC121

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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.: 2
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 Protein Mdm4 / Double minute 4 protein / Mdm2-like p53-binding protein / Protein Mdmx / p53-binding protein Mdm4


Mass: 4529.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15151
#3: 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.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Sodium citrate tribasic dihydrate, PEG3350, Bis-Tris propane pH8

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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: Mar 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→65.11 Å / Num. obs: 42044 / % possible obs: 99.3 % / Redundancy: 2 % / Biso Wilson estimate: 40.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.045 / Rrim(I) all: 0.064 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.1720.46630732140.7150.460.6511.493
8.93-65.111.80.01610795950.9980.0160.0237.699.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 2.105→56.264 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.64
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 4122 5.02 %random
Rwork0.2122 ---
obs0.2139 42044 99.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.18 Å2 / Biso mean: 54.6914 Å2 / Biso min: 23.27 Å2
Refinement stepCycle: final / Resolution: 2.105→56.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 45 179 3869
Biso mean--61.51 49.87 -
Num. residues----476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023718
X-RAY DIFFRACTIONf_angle_d0.4925022
X-RAY DIFFRACTIONf_chiral_restr0.031571
X-RAY DIFFRACTIONf_plane_restr0.002645
X-RAY DIFFRACTIONf_dihedral_angle_d13.5932279
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.105-2.12960.3781270.3725224683
2.1296-2.15550.36311250.33512708100
2.1555-2.18280.3261670.32542745100
2.1828-2.21150.32891610.3302262999
2.2115-2.24180.38731520.34682620100
2.2418-2.27390.46771490.4049274699
2.2739-2.30780.311520.29482683100
2.3078-2.34390.2891410.2672269799
2.3439-2.38230.32541310.26662697100
2.3823-2.42340.29841300.26232757100
2.4234-2.46740.28671230.25812669100
2.4674-2.51490.28581660.2682702100
2.5149-2.56620.32761260.25552691100
2.5662-2.6220.31361200.25062759100
2.622-2.6830.29021750.24642723100
2.683-2.75010.33711400.25072663100
2.7501-2.82450.27831300.24372739100
2.8245-2.90760.24081490.23662668100
2.9076-3.00140.25331400.23542752100
3.0014-3.10870.24371490.23112703100
3.1087-3.23310.29341520.234266599
3.2331-3.38030.24771500.21682705100
3.3803-3.55850.23391420.20062725100
3.5585-3.78140.24451360.19022693100
3.7814-4.07330.2541400.16272698100
4.0733-4.4830.14381390.15682745100
4.483-5.13130.18581250.15112688100
5.1313-6.46340.27051360.192746100
6.4634-56.2640.16761490.1708267699

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