[English] 日本語
Yorodumi
- PDB-1kwp: Crystal Structure of MAPKAP2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kwp
TitleCrystal Structure of MAPKAP2
ComponentsMAP Kinase Activated Protein Kinase 2
KeywordsTRANSFERASE / MAPKAP2 / protein kinase / signal transduction
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 / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity ...calcium-dependent protein serine/threonine kinase activity / macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity / regulation of interleukin-6 production / mitogen-activated protein kinase binding / positive regulation of macrophage cytokine production / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / cellular response to vascular endothelial growth factor stimulus / Regulation of HSF1-mediated heat shock response / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / calmodulin binding / intracellular signal transduction / ciliary basal body / protein phosphorylation / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / 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 ...MAP kinase activated protein kinase, C-terminal / 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
: / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMeng, W. / Swenson, L.L. / Fitzgibbon, M.J. / Hayakawa, K. / ter Haar, E. / Behrens, A.E. / Fulghum, J.R. / Lippke, J.A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of Mitogen-activated Protein Kinase-activated Protein (MAPKAP) Kinase 2 Suggests a Bifunctional Switch That Couples Kinase Activation with Nuclear Export
Authors: Meng, W. / Swenson, L.L. / Fitzgibbon, M.J. / Hayakawa, K. / Ter Haar, E. / Behrens, A.E. / Fulghum, J.R. / Lippke, J.A.
History
DepositionJan 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jul 4, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.5Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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: MAP Kinase Activated Protein Kinase 2
B: MAP Kinase Activated Protein Kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,06816
Polymers91,2592
Non-polymers2,80814
Water2,414134
1
A: MAP Kinase Activated Protein Kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0348
Polymers45,6301
Non-polymers1,4047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MAP Kinase Activated Protein Kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0348
Polymers45,6301
Non-polymers1,4047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: MAP Kinase Activated Protein Kinase 2
B: MAP Kinase Activated Protein Kinase 2
hetero molecules

A: MAP Kinase Activated Protein Kinase 2
B: MAP Kinase Activated Protein Kinase 2
hetero molecules

A: MAP Kinase Activated Protein Kinase 2
B: MAP Kinase Activated Protein Kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,20348
Polymers273,7786
Non-polymers8,42542
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area28790 Å2
ΔGint-1077 kcal/mol
Surface area79900 Å2
MethodPQS
Unit cell
Length a, b, c (Å)143.944, 143.944, 90.273
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-466-

HOH

21A-468-

HOH

31B-476-

HOH

-
Components

#1: Protein MAP Kinase Activated Protein Kinase 2 / MAPKAP2


Mass: 45629.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P49137, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.15
Details: 2 M Na/K phosphate, pH 5.15, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris1droppH7.8
2200 mM1dropNaCl
32 mMdithiothreitol1drop
45-10 mg/mlprotein1drop
52 Msodium potassium phospahte1reservoirpH5.15

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→32.6 Å / Num. all: 34168 / Num. obs: 34168 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 11.3 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 4.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.9 / Num. unique all: 2532 / Rsym value: 0.302 / % possible all: 100
Reflection
*PLUS
Num. obs: 17189 / % possible obs: 100 % / Num. measured all: 386514 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Rmerge(I) obs: 0.302

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNXrefinement
REFMACrefinement
CCP4(SCALA)data scaling
CNXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→32.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1702 -RANDOM
Rwork0.233 ---
all0.233 34168 --
obs0.233 34168 100 %-
Refinement stepCycle: LAST / Resolution: 2.8→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4751 0 14 134 4899
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg3.2
Software
*PLUS
Name: 'CNX AND REFMAC' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.233 / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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