[English] 日本語
Yorodumi
- PDB-6buu: Crystal structure of AKT1 (aa 144-480) with a bisubstrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6buu
TitleCrystal structure of AKT1 (aa 144-480) with a bisubstrate
Components
  • GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU
  • RAC-alpha serine/threonine-protein kinase
KeywordsTRANSFERASE / AKT1 / RAC-alpha serine/theronine-protein kinase / kinase / phosphorylated tail / semi-synthesis
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 / 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 ...glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / response to insulin-like growth factor stimulus / potassium channel activator activity / 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 / AKT phosphorylates targets in the nucleus / regulation of glycogen biosynthetic process / cellular response to oxidised low-density lipoprotein particle stimulus / regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / negative regulation of cilium assembly / positive regulation of I-kappaB phosphorylation / superior temporal gyrus development / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / response to fluid shear stress / RUNX2 regulates genes involved in cell migration / negative regulation of dopaminergic neuron differentiation / positive regulation of organ growth / maintenance of cell polarity / positive regulation of protein localization to centrosome / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / MTOR signalling / fibroblast migration / interleukin-18-mediated signaling pathway / positive regulation of sodium ion transport / positive regulation of cilium assembly / mammary gland epithelial cell differentiation / negative regulation of endopeptidase activity / negative regulation of protein acetylation / negative regulation of protein serine/threonine kinase activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / RAB GEFs exchange GTP for GDP on RABs / positive regulation of glucose metabolic process / tau-protein kinase / CRMPs in Sema3A signaling / heart valve development / positive regulation of endodeoxyribonuclease activity / regulation of microtubule-based process / response to growth factor / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of protein localization to cell surface / regulation of protein export from nucleus / protein serine/threonine kinase inhibitor activity / negative regulation of leukocyte cell-cell adhesion / phosphatidylinositol-3,4-bisphosphate binding / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / peripheral nervous system myelin maintenance / Maturation of nucleoprotein / sphingosine-1-phosphate receptor signaling pathway / cellular response to interleukin-3 / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / response to growth hormone / Wnt signalosome / negative regulation of protein localization to nucleus / anoikis / glycogen biosynthetic process / negative regulation of TOR signaling / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / labyrinthine layer blood vessel development / execution phase of apoptosis / response to food / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of cell-matrix adhesion / response to UV-A / regulation of myelination / regulation of postsynapse organization / regulation of axon extension / regulation of neuron projection development / G protein-coupled dopamine receptor signaling pathway / KSRP (KHSRP) binds and destabilizes mRNA
Similarity search - Function
Protein kinase B alpha, catalytic domain / Protein Kinase B, pleckstrin homology domain / Glycogen synthase kinase 3, catalytic domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. ...Protein kinase B alpha, catalytic domain / Protein Kinase B, pleckstrin homology domain / Glycogen synthase kinase 3, catalytic domain / Protein kinase, C-terminal / Protein kinase C terminal domain / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RAC-alpha serine/threonine-protein kinase / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
Model detailsMn+bisubstrate
AuthorsChu, N. / Gabelli, S.B. / Cole, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA74305 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA062924 United States
CitationJournal: Cell / Year: 2018
Title: Akt Kinase Activation Mechanisms Revealed Using Protein Semisynthesis.
Authors: Chu, N. / Salguero, A.L. / Liu, A.Z. / Chen, Z. / Dempsey, D.R. / Ficarro, S.B. / Alexander, W.M. / Marto, J.A. / Li, Y. / Amzel, L.M. / Gabelli, S.B. / Cole, P.A.
History
DepositionDec 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAC-alpha serine/threonine-protein kinase
B: RAC-alpha serine/threonine-protein kinase
F: GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU
G: GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0547
Polymers81,8484
Non-polymers2063
Water4,288238
1
A: RAC-alpha serine/threonine-protein kinase
F: GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0754
Polymers40,9242
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-23 kcal/mol
Surface area15830 Å2
MethodPISA
2
B: RAC-alpha serine/threonine-protein kinase
G: GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9793
Polymers40,9242
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-11 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.628, 56.267, 91.837
Angle α, β, γ (deg.)90.000, 105.100, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein RAC-alpha serine/threonine-protein kinase / Protein kinase B / PKB / Protein kinase B alpha / PKB alpha / Proto-oncogene c-Akt / RAC-PK-alpha


Mass: 39238.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKT1, PKB, RAC / Plasmid: pfastbac
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
Strain (production host): SF9
References: UniProt: P31749, non-specific serine/threonine protein kinase
#2: Protein/peptide GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU


Mass: 1685.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49841*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.68 Å3/Da / Density % sol: 54.18 % / Mosaicity: 1.039 ° / Mosaicity esd: 0.014 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG 3000, 0.1M Hepes HCL, 0.2M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 31906 / % possible obs: 94.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.046 / Rrim(I) all: 0.084 / Χ2: 2.995 / Net I/σ(I): 17.5 / Num. measured all: 96011
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.441.90.13910210.9530.1130.181.35861.9
2.44-2.492.10.13311940.9690.1050.171.41771.4
2.49-2.532.30.13113310.9680.0990.1651.39378.5
2.53-2.592.50.13314740.9620.0970.1661.63688.2
2.59-2.642.80.12616720.9720.0880.1551.5899
2.64-2.730.11216250.9750.0770.1371.81997.7
2.7-2.7730.10816650.9790.0740.1311.94199.9
2.77-2.853.10.10216760.9780.0690.1242.12799
2.85-2.933.10.09416530.9840.0640.1152.30199.5
2.93-3.023.20.08816840.9840.0590.1072.55299.5
3.02-3.133.20.08716900.9850.0580.1052.59499.5
3.13-3.263.30.07816670.9880.0510.0942.99199.5
3.26-3.413.30.07316630.9890.0470.0873.21599.5
3.41-3.583.30.06716830.9910.0430.083.61499.3
3.58-3.813.30.06716850.990.0440.084.10698.9
3.81-4.13.30.06416650.9920.0420.0774.10199
4.1-4.523.30.06216920.9920.0410.0754.56698.9
4.52-5.173.20.06217020.9920.0410.0754.32698.9
5.17-6.513.20.06116990.9910.040.0743.76299.6
6.51-502.90.05317650.9950.0370.0644.22498.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
REFMAC5.8.0135phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4EKK

4ekk


Resolution: 2.4→47 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2268 / WRfactor Rwork: 0.1818 / FOM work R set: 0.839 / SU B: 6.834 / SU ML: 0.162 / SU R Cruickshank DPI: 0.5097 / SU Rfree: 0.2665 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.51 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1382 4.7 %RANDOM
Rwork0.1831 ---
obs0.1854 28033 86.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.93 Å2 / Biso mean: 37.814 Å2 / Biso min: 8.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20.74 Å2
2---1.31 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 2.4→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 7 238 5743
Biso mean--63.25 33.83 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195687
X-RAY DIFFRACTIONr_bond_other_d0.0020.025347
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.997679
X-RAY DIFFRACTIONr_angle_other_deg1.039312330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9865.015668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42623.309275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2971542
X-RAY DIFFRACTIONr_chiral_restr0.1050.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026284
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021346
LS refinement shellResolution: 2.398→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 62 -
Rwork0.21 1341 -
all-1403 -
obs--56.3 %

+
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