[English] 日本語
Yorodumi
- PDB-6yr5: 14-3-3 sigma in complex with hDMX-367 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yr5
Title14-3-3 sigma in complex with hDMX-367 peptide
Components
  • 14-3-3 protein sigma
  • Protein Mdm4
KeywordsPEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / transcription repressor complex / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / DNA damage response, signal transduction by p53 class mediator / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Stabilization of p53 / negative regulation of protein catabolic process / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / intrinsic apoptotic signaling pathway in response to DNA damage / ubiquitin-protein transferase activity / Regulation of TP53 Degradation / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / protein-containing complex assembly / Oxidative Stress Induced Senescence / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cadherin binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / 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: 2.25 Å
AuthorsWolter, M. / Srdanovic, S. / Ottman, C. / Warriner, S. / Wilson, A.
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: Database references / Category: citation / citation_author
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,9959
Polymers112,8998
Non-polymers961
Water6,684371
1
A: 14-3-3 protein sigma
O: Protein Mdm4
B: 14-3-3 protein sigma
P: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5465
Polymers56,4504
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-40 kcal/mol
Surface area22770 Å2
MethodPISA
2
C: 14-3-3 protein sigma
Q: Protein Mdm4

D: 14-3-3 protein sigma
R: Protein Mdm4


Theoretical massNumber of molelcules
Total (without water)56,4504
Polymers56,4504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3930 Å2
ΔGint-30 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.950, 75.300, 78.390
Angle α, β, γ (deg.)95.150, 113.140, 93.840
Int Tables number1
Space group name H-MP1

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


Mass: 1681.894 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15151
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Bis-Tris propane pH 7, 0.2 M Sodium citrate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033208 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033208 Å / Relative weight: 1
ReflectionResolution: 2.1→74.53 Å / Num. obs: 75667 / % possible obs: 97.4 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.051 / Rrim(I) all: 0.125 / Net I/σ(I): 9.5
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
2.1-2.145.90.6732650844740.7970.2980.7392.896.4
10.5-71.56.80.08141276070.980.0350.08821.498.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
PHENIX1.12refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DAT

4dat


Resolution: 2.25→74.5 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.156 / SU ML: 0.128 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.186
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 2993 4.9 %RANDOM
Rwork0.1975 ---
obs0.1987 58664 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.17 Å2 / Biso mean: 31.365 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å2-0.27 Å20.1 Å2
2---1.32 Å2-0.1 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.25→74.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7324 0 5 371 7700
Biso mean--65.07 34.67 -
Num. residues----943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137439
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176973
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.64310034
X-RAY DIFFRACTIONr_angle_other_deg1.3991.5816140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22822.248387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74151343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.741555
X-RAY DIFFRACTIONr_chiral_restr0.0820.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021515
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 206 -
Rwork0.295 4295 -
all-4501 -
obs--96.32 %

+
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