[English] 日本語
Yorodumi
- PDB-7npg: Crystal structure of 14-3-3 sigma in complex with 20mer Amot-p130... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7npg
TitleCrystal structure of 14-3-3 sigma in complex with 20mer Amot-p130 peptide and fragment 22
Components
  • 14-3-3 protein sigma
  • Amot-p130 phosphopeptide (pS175)
KeywordsSIGNALING PROTEIN / protein-peptide complex fragment soaking
Function / homology
Function and homology information


establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / Regulation of CDH11 function / positive regulation of embryonic development / blood vessel endothelial cell migration / establishment of epithelial cell polarity / angiostatin binding / hippo signaling / negative regulation of vascular permeability / gastrulation with mouth forming second ...establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / Regulation of CDH11 function / positive regulation of embryonic development / blood vessel endothelial cell migration / establishment of epithelial cell polarity / angiostatin binding / hippo signaling / negative regulation of vascular permeability / gastrulation with mouth forming second / Signaling by Hippo / cell-cell junction assembly / regulation of small GTPase mediated signal transduction / 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 / endocytic vesicle / keratinocyte proliferation / positive regulation of cell size / phosphoserine residue binding / negative regulation of keratinocyte proliferation / Activation of BAD and translocation to mitochondria / bicellular tight junction / positive regulation of blood vessel endothelial cell migration / establishment of skin barrier / vasculogenesis / 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 / stress fiber / positive regulation of protein localization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of innate immune response / ruffle / protein sequestering activity / protein kinase A signaling / protein export from nucleus / regulation of cell migration / positive regulation of cell adhesion / negative regulation of angiogenesis / 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 / actin filament / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage / chemotaxis / protein localization / cell junction / lamellipodium / regulation of protein localization / signaling receptor activity / actin cytoskeleton organization / cytoplasmic vesicle / positive regulation of cell growth / angiogenesis / in utero embryonic development / regulation of cell cycle / cadherin binding / external side of plasma membrane / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Angiomotin / Angiomotin, C-terminal / : / Angiomotin C terminal / 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 ...Angiomotin / Angiomotin, C-terminal / : / Angiomotin C terminal / 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
Chem-K92 / 14-3-3 protein sigma / Angiomotin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsCentorrino, F. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: Curr Res Struct Biol / Year: 2022
Title: Fragment-based exploration of the 14-3-3/Amot-p130 interface.
Authors: Centorrino, F. / Andlovic, B. / Cossar, P. / Brunsveld, L. / Ottmann, C.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 2.0Jan 26, 2022Group: Atomic model / Database references / Category: atom_site / citation
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Amot-p130 phosphopeptide (pS175)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9207
Polymers30,4692
Non-polymers4515
Water7,008389
1
A: 14-3-3 protein sigma
P: Amot-p130 phosphopeptide (pS175)
hetero molecules

A: 14-3-3 protein sigma
P: Amot-p130 phosphopeptide (pS175)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,84114
Polymers60,9384
Non-polymers90310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5790 Å2
ΔGint-77 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.933, 112.272, 62.731
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-305-

MG

21A-768-

HOH

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AP

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


Mass: 28226.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31947
#2: Protein/peptide Amot-p130 phosphopeptide (pS175) / Angiomotin


Mass: 2242.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q4VCS5

-
Non-polymers , 5 types, 394 molecules

#3: Chemical ChemComp-K92 / 5-[3-(2-azanylethyl)imidazol-4-yl]-4-phenyl-thiophene-2-carboximidamide


Mass: 311.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.095 M Hepes pH 7.5, 26% PEG 400, 0.19 M CaCl2 and 5% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.37→41.83 Å / Num. obs: 61733 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 16.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.8
Reflection shellResolution: 1.37→1.39 Å / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3046 / CC1/2: 0.813

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.37→41.83 Å / SU ML: 0.1391 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.7345 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1706 3109 5.04 %
Rwork0.1548 58613 -
obs0.1556 61722 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.61 Å2
Refinement stepCycle: LAST / Resolution: 1.37→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 26 389 2298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812069
X-RAY DIFFRACTIONf_angle_d0.98742808
X-RAY DIFFRACTIONf_chiral_restr0.0618304
X-RAY DIFFRACTIONf_plane_restr0.0061373
X-RAY DIFFRACTIONf_dihedral_angle_d18.3255798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.28231350.28342651X-RAY DIFFRACTION99.96
1.39-1.410.23191460.22852596X-RAY DIFFRACTION100
1.41-1.440.2111500.2142637X-RAY DIFFRACTION99.96
1.44-1.460.22041360.19732657X-RAY DIFFRACTION99.89
1.46-1.490.19811520.18512606X-RAY DIFFRACTION99.93
1.49-1.520.17261320.17732637X-RAY DIFFRACTION99.96
1.52-1.560.1891310.18612654X-RAY DIFFRACTION99.96
1.56-1.590.21261430.16672640X-RAY DIFFRACTION99.96
1.59-1.630.17731380.15832650X-RAY DIFFRACTION100
1.63-1.680.16771240.1562653X-RAY DIFFRACTION100
1.68-1.730.15991450.1542651X-RAY DIFFRACTION100
1.73-1.780.1621410.15782635X-RAY DIFFRACTION100
1.78-1.850.18091240.15592707X-RAY DIFFRACTION100
1.85-1.920.17191370.15562633X-RAY DIFFRACTION100
1.92-2.010.18691580.1542656X-RAY DIFFRACTION100
2.01-2.110.16641330.14862673X-RAY DIFFRACTION100
2.11-2.240.16411330.14172691X-RAY DIFFRACTION100
2.24-2.420.16481500.13832661X-RAY DIFFRACTION100
2.42-2.660.16461400.14232669X-RAY DIFFRACTION100
2.66-3.050.15671480.15082712X-RAY DIFFRACTION100
3.05-3.840.1451440.13882720X-RAY DIFFRACTION100
3.84-41.830.17931690.16272824X-RAY DIFFRACTION99.9

+
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