[English] 日本語
Yorodumi
- PDB-2oza: Structure of p38alpha complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oza
TitleStructure of p38alpha complex
Components
  • MAP kinase-activated protein kinase 2
  • Mitogen-activated protein kinase 14
KeywordsSIGNALING PROTEIN/TRANSFERASE / SERINE/THREONINE KINASE / PROTEIN-PROTEIN COMPLEX / P38A / MK2 / SIGNALING PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA ...calcium-dependent protein serine/threonine kinase activity / macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / Regulation of MITF-M-dependent genes involved in pigmentation / activated TAK1 mediates p38 MAPK activation / Synthesis of Leukotrienes (LT) and Eoxins (EX) / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence / ADP signalling through P2Y purinoceptor 1 / Regulation of TP53 Activity through Phosphorylation / Myogenesis / regulation of tumor necrosis factor production / VEGFA-VEGFR2 Pathway / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity / regulation of interleukin-6 production / mitogen-activated protein kinase binding / regulation of synaptic membrane adhesion / positive regulation of macrophage cytokine production / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / positive regulation of myoblast fusion / cartilage condensation / cellular response to UV-B / toll-like receptor signaling pathway / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / D-glucose import / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / inner ear development / response to dietary excess / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / Regulation of HSF1-mediated heat shock response / JUN kinase activity / mitogen-activated protein kinase / chondrocyte differentiation / negative regulation of hippo signaling / positive regulation of myoblast differentiation / vascular endothelial growth factor receptor signaling pathway / skeletal muscle tissue development / stress-activated MAPK cascade / regulation of cellular response to heat / positive regulation of cardiac muscle cell proliferation / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / regulation of mRNA stability / positive regulation of interleukin-12 production / Neutrophil degranulation / response to cytokine / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / cellular response to ionizing radiation / positive regulation of D-glucose import / activated TAK1 mediates p38 MAPK activation / stem cell differentiation / response to insulin / placenta development / Regulation of TNFR1 signaling / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / bone development / cellular response to virus / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / glucose metabolic process / spindle pole / positive regulation of reactive oxygen species metabolic process / positive regulation of tumor necrosis factor production / osteoblast differentiation / kinase activity / MAPK cascade / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / Oxidative Stress Induced Senescence / angiogenesis / response to lipopolysaccharide / transcription by RNA polymerase II
Similarity search - Function
Protein kinase-like (PK-like) / MAP kinase activated protein kinase 2 / MAP kinase activated protein kinase, C-terminal / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Few Secondary Structures / Irregular ...Protein kinase-like (PK-like) / MAP kinase activated protein kinase 2 / MAP kinase activated protein kinase, C-terminal / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Few Secondary Structures / Irregular / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Mitogen-activated protein kinase 14 / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWhite, A. / Pargellis, C.A. / Studts, J.M. / Werneburg, B.G. / Farmer II, B.T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular basis of MAPK-activated protein kinase 2:p38 assembly
Authors: White, A. / Pargellis, C.A. / Studts, J.M. / Werneburg, B.G. / Farmer II, B.T.
History
DepositionFeb 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MAP kinase-activated protein kinase 2
B: Mitogen-activated protein kinase 14


Theoretical massNumber of molelcules
Total (without water)83,0832
Polymers83,0832
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-21 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.310, 83.310, 231.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a heterodimer containing one p38alpha and one MK2 molecules

-
Components

#1: Protein MAP kinase-activated protein kinase 2 / E.C.2.7.11.1 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAPK-2 / MK2


Mass: 40983.469 Da / Num. of mol.: 1 / Fragment: MK2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Protein Mitogen-activated protein kinase 14 / E.C.2.7.11.24 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha / CRK1


Mass: 42099.969 Da / Num. of mol.: 1 / Fragment: P38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P47811, mitogen-activated protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5 to 20% PEG 4000, 100mM Na Citrate, 5mM DTT, pH 6.0, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 29, 2004 / Details: SGX-CAT
RadiationMonochromator: SGX-CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→26.8 Å / Num. all: 23258 / Num. obs: 22784 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.115 / Χ2: 0.9 / Net I/σ(I): 8.8 / Scaling rejects: 19252
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.74 % / Mean I/σ(I) obs: 2.1 / Num. measured all: 12295 / Num. unique all: 1924 / Rsym value: 0.59 / Χ2: 1.07 / % possible all: 84.9

-
Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata processing
CNSrefinement
PDB_EXTRACT2data extraction
SGX-CATdata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→26.8 Å / FOM work R set: 0.721 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1110 4.8 %RANDOM
Rwork0.239 ---
all-23258 --
obs-22770 97.7 %-
Displacement parametersBiso mean: 72.691 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.7→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 0 60 5500
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.740.472420.433806848
2.74-2.790.405420.42847889
2.79-2.840.488530.426888941
2.84-2.890.618400.4359801020
2.89-2.940.441470.4059731020
2.94-30.468460.389861032
3-3.070.406580.3619851043
3.07-3.140.384430.3429771020
3.14-3.220.377430.29910161059
3.22-3.30.338490.2769821031
3.3-3.40.325430.2559911034
3.4-3.510.302530.27710141067
3.51-3.640.316620.2449721034
3.64-3.780.29500.22910131063
3.78-3.950.279490.21410041053
3.95-4.160.28670.2119901057
4.16-4.420.24510.19110071058
4.42-4.770.278560.19310121068
4.77-5.250.262450.20510351080
5.25-60.232460.22810541100
6-7.570.283690.20510441113
7.57-500.010.244560.19510841140
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
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