[English] 日本語
Yorodumi
- PDB-1h10: HIGH RESOLUTION STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF PR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h10
TitleHIGH RESOLUTION STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN OF PROTEIN KINASE B/AKT BOUND TO INS(1,3,4,5)-TETRAKISPHOPHATE
ComponentsRAC-ALPHA SERINE/THREONINE KINASE
KeywordsTRANSFERASE / SIGNALLING PROTEIN / PHOSPHOINOSITIDES / PROTEIN KINASE B / PLECKSTRIN / INOSITOL TETRAKISPHOPHATE / PHOSPHORYLATION / SERINE/THREONINE PROTEIN KINASE
Function / homology
Function and homology information


regulation of tRNA methylation / negative regulation of protein maturation / response to insulin-like growth factor stimulus / regulation of glycogen biosynthetic process / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / negative regulation of lymphocyte migration / cellular response to rapamycin / maintenance of protein location in mitochondrion / cellular response to decreased oxygen levels ...regulation of tRNA methylation / negative regulation of protein maturation / response to insulin-like growth factor stimulus / regulation of glycogen biosynthetic process / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / negative regulation of lymphocyte migration / cellular response to rapamycin / maintenance of protein location in mitochondrion / cellular response to decreased oxygen levels / maternal placenta development / regulation of type B pancreatic cell development / AKT-mediated inactivation of FOXO1A / negative regulation of long-chain fatty acid import across plasma membrane / Negative regulation of the PI3K/AKT network / potassium channel activator activity / establishment of protein localization to mitochondrion / AKT phosphorylates targets in the nucleus / negative regulation of fatty acid beta-oxidation / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / negative regulation of cilium assembly / cellular response to peptide / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of organ growth / positive regulation of TORC2 signaling / RUNX2 regulates genes involved in cell migration / interleukin-18-mediated signaling pathway / response to fluid shear stress / fibroblast migration / MTOR signalling / positive regulation of sodium ion transport / mammary gland epithelial cell differentiation / response to growth factor / positive regulation of glucose metabolic process / cellular response to granulocyte macrophage colony-stimulating factor stimulus / RAB GEFs exchange GTP for GDP on RABs / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of leukocyte cell-cell adhesion / positive regulation of protein localization to cell surface / peripheral nervous system myelin maintenance / glycogen biosynthetic process / sphingosine-1-phosphate receptor signaling pathway / positive regulation of endodeoxyribonuclease activity / response to growth hormone / cell migration involved in sprouting angiogenesis / positive regulation of fibroblast migration / anoikis / protein serine/threonine kinase inhibitor activity / mammalian oogenesis stage / regulation of postsynapse organization / labyrinthine layer blood vessel development / AKT phosphorylates targets in the cytosol / activation-induced cell death of T cells / TORC2 complex binding / regulation of myelination / response to food / response to UV-A / Regulation of TP53 Activity through Association with Co-factors / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / KSRP (KHSRP) binds and destabilizes mRNA / execution phase of apoptosis / phosphorylation / apoptotic mitochondrial changes / Co-inhibition by CTLA4 / negative regulation of macroautophagy / negative regulation of cGAS/STING signaling pathway / cellular response to stress / regulation of neuron projection development / negative regulation of release of cytochrome c from mitochondria / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of PERK-mediated unfolded protein response / phosphatidylinositol-3,4,5-trisphosphate binding / behavioral response to pain / TOR signaling / positive regulation of protein metabolic process / Regulation of localization of FOXO transcription factors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of Notch signaling pathway / cellular response to vascular endothelial growth factor stimulus / CD28 dependent PI3K/Akt signaling / positive regulation of blood vessel endothelial cell migration / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of fat cell differentiation / Mitochondrial unfolded protein response (UPRmt) / positive regulation of glycogen biosynthetic process / vascular endothelial cell response to laminar fluid shear stress / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of lipid biosynthetic process / Cyclin E associated events during G1/S transition / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Cyclin A:Cdk2-associated events at S phase entry / eNOS activation / positive regulation of peptidyl-serine phosphorylation / negative regulation of proteolysis / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Regulation of TP53 Activity through Acetylation
Similarity search - Function
Protein kinase B alpha, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain ...Protein kinase B alpha, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / RAC-alpha serine/threonine-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.4 Å
AuthorsThomas, C.C. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
CitationJournal: Curr.Biol. / Year: 2002
Title: High Resolution Structure of the Pleckstrin Homology Domain of Protein Kinase B/Akt Bound to Phosphatidylinositol (3,4,5)-Trisphosphate
Authors: Thomas, C.C. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
History
DepositionJul 1, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAC-ALPHA SERINE/THREONINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4402
Polymers14,9401
Non-polymers5001
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.868, 34.351, 44.293
Angle α, β, γ (deg.)90.00, 115.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2094-

HOH

-
Components

#1: Protein RAC-ALPHA SERINE/THREONINE KINASE / PROTEIN KINASE B (ALPHA) PLECKSTRIN HOMOLOGY / RAC-PK-ALPHA / AKT1 / PKB / RAC


Mass: 14940.391 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 1-123
Source method: isolated from a genetically manipulated source
Details: BOUND TO INS(1,3,4,5)-TETRAKISPHOPHATE, SELENOMETHIONINE DERIVATIVE
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P31749, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O18P4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGENERAL PROTEIN KINASE, PHOSPHORYLATION OF MANY KNOWN PROTEINS.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.07 %
Crystal growpH: 4.2
Details: 0.25M AMMONIUM ACETATE, 30% PEG 4000,0.1M SODIUM ACETATE (PH 4.6)
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.5 mg/mlprotein1drop
20.25 Mammonium acetate1reservoir
330 %PEG40001reservoir
40.1 Msodium acetate1reservoirpH4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9786
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.4→15 Å / Num. obs: 21933 / % possible obs: 97.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 30.8
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 6.7 / % possible all: 83.3
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 15 Å / Redundancy: 3.8 % / Num. measured all: 83520 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 83.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 6.7

-
Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.4→15 Å / Num. parameters: 11393 / Num. restraintsaints: 10950 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: REFINEMENT USING CNS AND THEN SHELXL -97
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 914 5 %RANDOM
obs0.1254 -97.8 %-
all-83520 --
Refine analyzeOccupancy sum hydrogen: 943 / Occupancy sum non hydrogen: 1249.5
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 28 238 1250
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d2.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.033
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0.065
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.125 / Rfactor Rfree: 0.175 / Rfactor Rwork: 0.125
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.046

+
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