[English] 日本語
Yorodumi
- PDB-3ulc: Crystal structure of the pleckstrin homology domain of Saccharomy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ulc
TitleCrystal structure of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1, a TORC2 subunit, in the P3121 crystal form
ComponentsTarget of rapamycin complex 2 subunit AVO1
KeywordsMEMBRANE PROTEIN / PH domain / membrane localization
Function / homology
Function and homology information


PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / Regulation of TP53 Degradation / TORC2 signaling / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability / TORC2 complex / vacuolar membrane / TOR signaling / phosphatidylinositol-4,5-bisphosphate binding ...PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / Regulation of TP53 Degradation / TORC2 signaling / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability / TORC2 complex / vacuolar membrane / TOR signaling / phosphatidylinositol-4,5-bisphosphate binding / regulation of cell growth / molecular adaptor activity / plasma membrane / cytoplasm
Similarity search - Function
TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Target of rapamycin complex 2 subunit AVO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPan, D. / Matsuura, Y.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structures of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1 and its human orthologue Sin1, an essential subunit of TOR complex 2
Authors: Pan, D. / Matsuura, Y.
History
DepositionNov 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Target of rapamycin complex 2 subunit AVO1


Theoretical massNumber of molelcules
Total (without water)14,6091
Polymers14,6091
Non-polymers00
Water362
1
A: Target of rapamycin complex 2 subunit AVO1

A: Target of rapamycin complex 2 subunit AVO1


Theoretical massNumber of molelcules
Total (without water)29,2172
Polymers29,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area4350 Å2
ΔGint-14 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.917, 60.917, 84.096
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Target of rapamycin complex 2 subunit AVO1 / TORC2 subunit AVO1 / Adheres voraciously to TOR2 protein 1


Mass: 14608.734 Da / Num. of mol.: 1 / Fragment: PH domain, residues 1056-1176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: AVO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08236
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris-HCl, 6% PEG8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2009
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→32.88 Å / Num. all: 4709 / Num. obs: 4563 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 3.7 / % possible all: 84

-
Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ULB

3ulb


Resolution: 2.8→28.64 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.838 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 206 4.5 %RANDOM
Rwork0.2436 ---
all0.2455 4709 --
obs0.2455 4563 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.71 Å2 / Biso mean: 57.7293 Å2 / Biso min: 24.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 0 2 808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02823
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.9321113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.496597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35322.10538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14215137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.609157
X-RAY DIFFRACTIONr_chiral_restr0.1050.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021613
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 12 -
Rwork0.359 220 -
all-232 -
obs--78.91 %

+
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