[English] 日本語
Yorodumi
- PDB-5lx2: Lt 14-3-3 in complex with PI4KIIIB peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lx2
TitleLt 14-3-3 in complex with PI4KIIIB peptide
Components
  • KLTH0G14146p
  • Phosphatidylinositol 4-kinase beta
KeywordsTRANSFERASE / phosphoserin / kinase / regulation
Function / homology
Function and homology information


1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol biosynthetic process / lysosome organization / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / inner ear development / 14-3-3 protein binding ...1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol biosynthetic process / lysosome organization / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / inner ear development / 14-3-3 protein binding / receptor-mediated endocytosis / mitochondrial outer membrane / endosome / phosphorylation / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / PI4KB/PIK1, accessory (PIK) domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. ...: / PI4KB/PIK1, accessory (PIK) domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / 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 / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol 4-kinase beta / KLTH0G14146p / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesLachancea thermotolerans (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.579 Å
AuthorsBoura, E. / Eisenreichova, A.
CitationJournal: To Be Published
Title: Lt 14-3-3 in complex with PI4KIIIB peptide
Authors: Boura, E. / Eisenreichova, A.
History
DepositionSep 19, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionNov 16, 2016ID: 5LI5
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KLTH0G14146p
B: Phosphatidylinositol 4-kinase beta


Theoretical massNumber of molelcules
Total (without water)29,3022
Polymers29,3022
Non-polymers00
Water54030
1
A: KLTH0G14146p
B: Phosphatidylinositol 4-kinase beta

A: KLTH0G14146p
B: Phosphatidylinositol 4-kinase beta


Theoretical massNumber of molelcules
Total (without water)58,6034
Polymers58,6034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3900 Å2
ΔGint-22 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.063, 123.671, 38.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein KLTH0G14146p


Mass: 28603.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus)
Gene: KLTH0G14146g / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5DN49
#2: Protein/peptide Phosphatidylinositol 4-kinase beta


Mass: 697.651 Da / Num. of mol.: 1 / Fragment: UNP residues 304-309 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A0A0B4J1S8, UniProt: Q9UBF8*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: MES, PEG 8000, ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.579→44.49 Å / Num. obs: 10043 / % possible obs: 98.35 % / Redundancy: 3.9 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1671 / Net I/σ(I): 6.5
Reflection shellResolution: 2.579→2.671 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 1.56 / CC1/2: 0.506 / % possible all: 98.25

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LHO

5lho
PDB Unreleased entry


Resolution: 2.579→44.491 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2627 503 5.01 %
Rwork0.2027 --
obs0.2057 10040 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.579→44.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 0 30 1927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021927
X-RAY DIFFRACTIONf_angle_d0.5242608
X-RAY DIFFRACTIONf_dihedral_angle_d11.443716
X-RAY DIFFRACTIONf_chiral_restr0.023299
X-RAY DIFFRACTIONf_plane_restr0.002333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5788-2.83820.36671210.27342291X-RAY DIFFRACTION98
2.8382-3.24880.32171240.25312358X-RAY DIFFRACTION98
3.2488-4.09270.22921250.18522371X-RAY DIFFRACTION99
4.0927-44.49750.23561330.17662517X-RAY DIFFRACTION98

+
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