[English] 日本語
Yorodumi
- PDB-4yno: Crystal structure of MAPK13 at INACTIVE FORM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yno
TitleCrystal structure of MAPK13 at INACTIVE FORM
ComponentsMitogen-activated protein kinase 13P38 mitogen-activated protein kinases
KeywordsTRANSFERASE / P38 KINASE
Function / homology
Function and homology information


cellular response to anisomycin / cellular response to sorbitol / cellular response to sodium arsenite / response to osmotic stress / DSCAM interactions / MAP kinase activity / mitogen-activated protein kinase / cellular response to interleukin-1 / stress-activated MAPK cascade / p38MAPK events ...cellular response to anisomycin / cellular response to sorbitol / cellular response to sodium arsenite / response to osmotic stress / DSCAM interactions / MAP kinase activity / mitogen-activated protein kinase / cellular response to interleukin-1 / stress-activated MAPK cascade / p38MAPK events / NOD1/2 Signaling Pathway / cellular response to hydrogen peroxide / VEGFA-VEGFR2 Pathway / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cellular response to UV / peptidyl-serine phosphorylation / intracellular signal transduction / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase 13 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Mitogen-activated protein kinase 13 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMiller, C.A. / Brett, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P50-HL107183 United States
Citation
Journal: J.Clin.Invest. / Year: 2012
Title: IL-13-induced airway mucus production is attenuated by MAPK13 inhibition.
Authors: Alevy, Y.G. / Patel, A.C. / Romero, A.G. / Patel, D.A. / Tucker, J. / Roswit, W.T. / Miller, C.A. / Heier, R.F. / Byers, D.E. / Brett, T.J. / Holtzman, M.J.
#1: Journal: To Be Published
Title: The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation
Authors: Yurtsever, Z. / Scheaffer, S.M. / Romero, A.G. / Holtzman, M.J. / Brett, T.J.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionApr 8, 2015ID: 4EXU
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase 13


Theoretical massNumber of molelcules
Total (without water)42,6341
Polymers42,6341
Non-polymers00
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.923, 69.405, 92.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Mitogen-activated protein kinase 13 / P38 mitogen-activated protein kinases / MAPK 13 / Mitogen-activated protein kinase p38 delta / MAP kinase p38 delta / Stress-activated ...MAPK 13 / Mitogen-activated protein kinase p38 delta / MAP kinase p38 delta / Stress-activated protein kinase 4


Mass: 42633.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK13, PRKM13, SAPK4 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 (DE3)
References: UniProt: O15264, mitogen-activated protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50 MM AMMONIUM TARTRATE, 18% PEG 3350

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.007 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2011
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 43897 / Num. obs: 43897 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 29.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 4.1 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3COI

3coi


Resolution: 1.7→36.839 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 2189 5.03 %Random
Rwork0.1964 ---
obs0.1979 43514 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→36.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 0 315 3092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072846
X-RAY DIFFRACTIONf_angle_d1.0983846
X-RAY DIFFRACTIONf_dihedral_angle_d13.2951070
X-RAY DIFFRACTIONf_chiral_restr0.043420
X-RAY DIFFRACTIONf_plane_restr0.005488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6996-1.73660.28481380.24272500X-RAY DIFFRACTION98
1.7366-1.7770.26411320.22162558X-RAY DIFFRACTION100
1.777-1.82140.23271360.20952550X-RAY DIFFRACTION100
1.8214-1.87070.241240.20822570X-RAY DIFFRACTION100
1.8707-1.92570.23111390.19982572X-RAY DIFFRACTION100
1.9257-1.98780.24091380.19762554X-RAY DIFFRACTION100
1.9878-2.05890.22661220.19262598X-RAY DIFFRACTION100
2.0589-2.14130.2111450.19222563X-RAY DIFFRACTION100
2.1413-2.23880.26291380.19382577X-RAY DIFFRACTION100
2.2388-2.35680.18531200.19732629X-RAY DIFFRACTION100
2.3568-2.50440.22891280.21262604X-RAY DIFFRACTION100
2.5044-2.69770.22811470.21042586X-RAY DIFFRACTION100
2.6977-2.96910.25681350.21222630X-RAY DIFFRACTION100
2.9691-3.39850.23651360.2062637X-RAY DIFFRACTION100
3.3985-4.28070.21831620.17662618X-RAY DIFFRACTION99
4.2807-36.84760.19521490.18332579X-RAY DIFFRACTION93

+
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