[English] 日本語
Yorodumi
- PDB-2uvm: Structure of PKBalpha PH domain in complex with a novel inositol ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2uvm
TitleStructure of PKBalpha PH domain in complex with a novel inositol headgroup surrogate, benzene 1,2,3,4-tetrakisphosphate
ComponentsRAC-ALPHA SERINE/THREONINE-PROTEIN KINASE
KeywordsTRANSFERASE / GLYCOGEN BIOSYNTHESIS / TRANSLATION REGULATION / SERINE/THREONINE-PROTEIN KINASE / PHOSPHOINOSITIDE / PROTEIN KINASE B / GLUCOSE METABOLISM / NUCLEAR PROTEIN / CELL SIGNALLING / PHOSPHORYLATION / NUCLEOTIDE-BINDING / GLYCOGEN METABOLISM / KINASE / CANCER / INOSITOL / APOPTOSIS / TRANSPORT / CARBOHYDRATE METABOLISM / PH DOMAIN / ATP-BINDING / SUGAR TRANSPORT
Function / homology
Function and homology information


glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / response to insulin-like growth factor stimulus / potassium channel activator activity / response to UV-A / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / maintenance of protein location in mitochondrion / negative regulation of lymphocyte migration / cellular response to decreased oxygen levels ...glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / response to insulin-like growth factor stimulus / potassium channel activator activity / response to UV-A / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / maintenance of protein location in mitochondrion / negative regulation of lymphocyte migration / cellular response to decreased oxygen levels / regulation of type B pancreatic cell development / AKT-mediated inactivation of FOXO1A / maternal placenta development / Negative regulation of the PI3K/AKT network / negative regulation of long-chain fatty acid import across plasma membrane / establishment of protein localization to mitochondrion / negative regulation of fatty acid beta-oxidation / regulation of glycogen biosynthetic process / AKT phosphorylates targets in the nucleus / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cilium assembly / positive regulation of I-kappaB phosphorylation / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / response to fluid shear stress / RUNX2 regulates genes involved in cell migration / positive regulation of organ growth / cellular response to peptide / fibroblast migration / interleukin-18-mediated signaling pathway / MTOR signalling / positive regulation of sodium ion transport / mammary gland epithelial cell differentiation / negative regulation of endopeptidase activity / negative regulation of protein serine/threonine kinase activity / RAB GEFs exchange GTP for GDP on RABs / positive regulation of glucose metabolic process / response to growth factor / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of protein localization to cell surface / positive regulation of endodeoxyribonuclease activity / negative regulation of leukocyte cell-cell adhesion / phosphatidylinositol-3,4-bisphosphate binding / peripheral nervous system myelin maintenance / protein serine/threonine kinase inhibitor activity / sphingosine-1-phosphate receptor signaling pathway / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / response to growth hormone / anoikis / glycogen biosynthetic process / positive regulation of cyclin-dependent protein serine/threonine kinase activity / AKT phosphorylates targets in the cytosol / labyrinthine layer blood vessel development / response to food / non-canonical NF-kappaB signal transduction / regulation of myelination / Cyclin E associated events during G1/S transition / regulation of postsynapse organization / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / KSRP (KHSRP) binds and destabilizes mRNA / execution phase of apoptosis / Regulation of TP53 Activity through Association with Co-factors / negative regulation of macroautophagy / positive regulation of fat cell differentiation / positive regulation of G1/S transition of mitotic cell cycle / CTLA4 inhibitory signaling / mammalian oogenesis stage / negative regulation of cGAS/STING signaling pathway / activation-induced cell death of T cells / negative regulation of Notch signaling pathway / regulation of neuron projection development / negative regulation of release of cytochrome c from mitochondria / Cyclin A:Cdk2-associated events at S phase entry / behavioral response to pain / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / apoptotic mitochondrial changes / phosphatidylinositol-3,4,5-trisphosphate binding / Regulation of localization of FOXO transcription factors / cellular response to epidermal growth factor stimulus / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of glycogen biosynthetic process / cellular response to cadmium ion / Activation of BAD and translocation to mitochondria / TOR signaling / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / eNOS activation / canonical NF-kappaB signal transduction / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / lipopolysaccharide-mediated signaling pathway / negative regulation of protein ubiquitination / 14-3-3 protein binding / Regulation of TP53 Activity through Acetylation / striated muscle cell differentiation / positive regulation of endothelial cell proliferation / regulation of mRNA stability
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. / Serine/Threonine protein kinases, catalytic domain / Protein kinase 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
Chem-GVF / RAC-alpha serine/threonine-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKomander, D. / Mills, S.J. / Trusselle, M.N. / Safrany, S.T. / van Aalten, D.M.F. / Potter, B.V.L.
CitationJournal: Acs Chem.Biol. / Year: 2007
Title: Novel Inositol Phospholipid Headgroup Surrogate Crystallised in the Pleckstrin Homology Domain of Protein Kinase Balpha.
Authors: Mills, S.J. / Komander, D. / Trusselle, M.N. / Safrany, S.T. / Van Aalten, D.M.F. / Potter, B.V.L.
History
DepositionMar 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,1723
Polymers14,6871
Non-polymers4852
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.029, 34.040, 44.944
Angle α, β, γ (deg.)90.00, 112.25, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein RAC-ALPHA SERINE/THREONINE-PROTEIN KINASE / PROTEIN KINASE B ALPHA / RAC-PK-ALPHA / PROTEIN KINASE B / PKB / C-AKT


Mass: 14686.589 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY (PH) DOMAIN, RESIDUES 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P31749, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GVF / BENZENE-1,2,3,4-TETRAYL TETRAKIS[DIHYDROGEN (PHOSPHATE)]


Mass: 462.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O16P4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.96 Å3/Da / Density % sol: 37 %
Crystal growpH: 5
Details: 25-30% POLYETHYLENE GLYCOL 3000, 0.1 M SODIUM ACETATE TRIHYDRATE [PH 4.4-5.0], 0.2 M AMMONIUM ACETATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.94→15 Å / Num. obs: 7781 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 4.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.5
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.2 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H10

1h10


Resolution: 1.94→14.98 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1108126.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: C-TERMINUS DISORDERED. SOME DISORDERED RESIDUES WERE MODELLED AS ALA.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 493 6.5 %RANDOM
Rwork0.252 ---
obs0.252 7635 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1029 Å2 / ksol: 0.368238 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å23.42 Å2
2--5.67 Å20 Å2
3----5.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.94→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms929 0 27 53 1009
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 79 6.3 %
Rwork0.263 1169 -
obs--90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BENZIP4.PARBENZIP4.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

+
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://pdbjlvh1.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