[English] 日本語
Yorodumi
- PDB-2x18: The crystal structure of the PH domain of human AKT3 protein kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x18
TitleThe crystal structure of the PH domain of human AKT3 protein kinase
ComponentsRAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
KeywordsTRANSFERASE / KINASE / MEMBRANE / ATP-BINDING
Function / homology
Function and homology information


positive regulation of artery morphogenesis / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / AKT phosphorylates targets in the nucleus / RUNX2 regulates genes involved in cell migration / mitochondrial genome maintenance / RAB GEFs exchange GTP for GDP on RABs / brain morphogenesis / AKT phosphorylates targets in the cytosol / positive regulation of vascular endothelial cell proliferation ...positive regulation of artery morphogenesis / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / AKT phosphorylates targets in the nucleus / RUNX2 regulates genes involved in cell migration / mitochondrial genome maintenance / RAB GEFs exchange GTP for GDP on RABs / brain morphogenesis / AKT phosphorylates targets in the cytosol / positive regulation of vascular endothelial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of cell migration involved in sprouting angiogenesis / CTLA4 inhibitory signaling / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of cellular senescence / CD28 dependent PI3K/Akt signaling / Regulation of localization of FOXO transcription factors / positive regulation of cell size / positive regulation of TOR signaling / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of blood vessel endothelial cell migration / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Transcriptional and post-translational regulation of MITF-M expression and activity / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / homeostasis of number of cells within a tissue / Regulation of TP53 Activity through Acetylation / positive regulation of endothelial cell proliferation / FLT3 Signaling / Downregulation of ERBB2:ERBB3 signaling / VEGFR2 mediated vascular permeability / TP53 Regulates Metabolic Genes / Regulation of PTEN stability and activity / positive regulation of angiogenesis / G beta:gamma signalling through PI3Kgamma / KEAP1-NFE2L2 pathway / Regulation of TP53 Degradation / PIP3 activates AKT signaling / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Protein kinase B gamma, 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 gamma, 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
RAC-gamma serine/threonine-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsVollmar, M. / Wang, J. / Zhang, Y. / Elkins, J.M. / Burgess-Brown, N. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Vollmar, M. / Wang, J. / Zhang, Y. / Elkins, J.M. / Burgess-Brown, N. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: The Crystal Structure of the Ph Domain of Human Akt3 Protein Kinase
Authors: Vollmar, M. / Wang, J. / Zhang, Y. / Elkins, J.M. / Burgess-Brown, N. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S.
History
DepositionDec 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 20, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
B: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
C: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
D: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
E: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
F: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
G: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
H: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,25912
Polymers114,3068
Non-polymers9534
Water30,9321717
1
A: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5272
Polymers14,2881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)14,2881
Polymers14,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)14,2881
Polymers14,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)14,2881
Polymers14,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5272
Polymers14,2881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5272
Polymers14,2881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)14,2881
Polymers14,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5272
Polymers14,2881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.475, 62.401, 71.411
Angle α, β, γ (deg.)111.47, 102.75, 94.36
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE / RAC-PK-GAMMA / PROTEIN KINASE AKT-3 / PROTEIN KINASE B GAMMA / PKB GAMMA / STK-2 / AKT3


Mass: 14288.233 Da / Num. of mol.: 8 / Fragment: PH DOMAIN, RESIDUES 466-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: Q9Y243, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1717 / 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: 2.45 Å3/Da / Density % sol: 49.81 % / Description: NONE
Crystal growDetails: 0.2M PROLINE, 0.1M HEPES PH 7.5, 10% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.46→64.03 Å / Num. obs: 164858 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UNP

1unp


Resolution: 1.46→64.03 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.003 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.23377 8269 5 %RANDOM
Rwork0.18934 ---
obs0.19156 156074 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.22 Å2-0.22 Å2
2---0.35 Å20.01 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.46→64.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7506 0 28 1717 9251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227910
X-RAY DIFFRACTIONr_bond_other_d0.0010.025514
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9510741
X-RAY DIFFRACTIONr_angle_other_deg2.369313469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62224.03402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.619151440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9651568
X-RAY DIFFRACTIONr_chiral_restr0.1190.21141
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218643
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021619
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.55734651
X-RAY DIFFRACTIONr_mcbond_other0.8331816
X-RAY DIFFRACTIONr_mcangle_it3.83557621
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.1983259
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.652113108
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 578 -
Rwork0.341 11046 -
obs--93.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08030.3079-0.13770.69910.07350.542-0.0024-0.0904-0.02460.06890.00290.02070.02650.0325-0.00050.00960.00760.00270.02010.00230.002328.760892.472614.85
20.46060.19250.24860.6275-0.13810.825-0.0065-0.05870.0270.09190.030.0190.0379-0.0527-0.02350.02850.0107-0.00290.0298-0.00570.007462.884760.605115.1801
30.60860.2911-0.08170.37330.15890.96070.0412-0.06690.02130.0492-0.02180.0348-0.00130.0031-0.01940.00830.0010.00450.0207-0.0050.007660.781692.03415.0711
40.47330.2424-0.06620.65080.40370.92030.00630.06110.0092-0.070.01260.0291-0.05520.0144-0.01890.01850.0067-0.00680.013-0.00170.008426.070887.9741-12.8494
50.72590.56410.0140.9313-0.14970.20750.0541-0.0526-0.030.1145-0.09570.051-0.02410.06240.04160.0164-0.00690.0070.04170.0090.041230.339260.563515.4946
60.58820.20870.02621.2788-0.04770.55270.00530.04880.0114-0.0915-0.01560.00020.0120.00880.01030.01230.0063-0.00150.00750.00070.003458.271857.5491-12.7165
70.47130.19120.06320.57590.01740.9694-0.01170.04790.0288-0.06580.01970.03230.0018-0.008-0.00810.01380.0027-0.00660.00810.00180.006357.399888.1157-12.8178
80.62230.4032-0.20441.0052-0.04910.4241-0.04170.06820.0114-0.07120.0265-0.02970.04150.00720.01520.01870.0032-0.00390.01210.00150.009527.917958.5649-13.5134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 114
2X-RAY DIFFRACTION2B4 - 117
3X-RAY DIFFRACTION3C4 - 118
4X-RAY DIFFRACTION4D4 - 118
5X-RAY DIFFRACTION5E3 - 118
6X-RAY DIFFRACTION6F3 - 113
7X-RAY DIFFRACTION7G4 - 118
8X-RAY DIFFRACTION8H3 - 118

+
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