[English] 日本語
Yorodumi
- PDB-4zsj: MITOGEN ACTIVATED PROTEIN KINASE 7 IN COMPLEX WITH INHIBITOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zsj
TitleMITOGEN ACTIVATED PROTEIN KINASE 7 IN COMPLEX WITH INHIBITOR
ComponentsMitogen-activated protein kinase 7
KeywordsTRANSFERASE / KINASE / INHIBITOR
Function / homology
Function and homology information


Signalling to ERK5 / negative regulation of response to cytokine stimulus / negative regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of heterotypic cell-cell adhesion / calcineurin-NFAT signaling cascade / negative regulation of smooth muscle cell apoptotic process / cellular response to laminar fluid shear stress / Gastrin-CREB signalling pathway via PKC and MAPK / ERKs are inactivated / mitogen-activated protein kinase binding ...Signalling to ERK5 / negative regulation of response to cytokine stimulus / negative regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of heterotypic cell-cell adhesion / calcineurin-NFAT signaling cascade / negative regulation of smooth muscle cell apoptotic process / cellular response to laminar fluid shear stress / Gastrin-CREB signalling pathway via PKC and MAPK / ERKs are inactivated / mitogen-activated protein kinase binding / negative regulation of calcineurin-NFAT signaling cascade / ERK/MAPK targets / cAMP-mediated signaling / RET signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / MAP kinase activity / mitogen-activated protein kinase / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cellular response to transforming growth factor beta stimulus / positive regulation of protein metabolic process / PML body / cellular response to hydrogen peroxide / cellular response to growth factor stimulus / negative regulation of inflammatory response / MAPK cascade / Senescence-Associated Secretory Phenotype (SASP) / cell differentiation / intracellular signal transduction / cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...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 / 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
Chem-4R0 / Mitogen-activated protein kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsTucker, J. / Ogg, D.J.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Discovery of a novel allosteric inhibitor-binding site in ERK5: comparison with the canonical kinase hinge ATP-binding site.
Authors: Chen, H. / Tucker, J. / Wang, X. / Gavine, P.R. / Phillips, C. / Augustin, M.A. / Schreiner, P. / Steinbacher, S. / Preston, M. / Ogg, D.
History
DepositionMay 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0866
Polymers39,4081
Non-polymers6775
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-0 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.040, 93.040, 110.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-698-

HOH

-
Components

#1: Protein Mitogen-activated protein kinase 7 / MAPK 7 / Big MAP kinase 1 / BMK-1 / Extracellular signal-regulated kinase 5 / ERK-5


Mass: 39408.367 Da / Num. of mol.: 1 / Fragment: UNP residues 50-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK7, BMK1, ERK5, PRKM7 / Plasmid: pFastBac HT A / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13164, mitogen-activated protein kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-4R0 / 3-amino-5-[(4-chloro-3-methylphenyl)amino]-N-(propan-2-yl)-1H-1,2,4-triazole-1-carboxamide


Mass: 308.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17ClN6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25 / Details: 4-6 % w/v PEG 6000, 0.1 M MES, 5 mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.48→71.2 Å / Num. obs: 17842 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 55.35 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.1
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 3.5 / % possible all: 99.8

-
Processing

Software
NameClassification
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house Erk5/MAPK7 structure

Resolution: 2.48→71.2 Å / SU R Cruickshank DPI: 0.316 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 0.378 / SU Rfree Blow DPI: 0.247 / SU Rfree Cruickshank DPI: 0.238
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 907 5.1 %Random selection
Rwork0.1671 ---
obs0.1701 17792 99.9 %-
Displacement parametersBiso mean: 49.09 Å2
Baniso -1Baniso -2Baniso -3
1--4.3531 Å20 Å20 Å2
2---4.3531 Å20 Å2
3---8.7063 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 2.48→71.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 45 261 3028
LS refinement shellResolution: 2.48→2.63 Å
RfactorNum. reflection% reflection
Rfree0.293 150 5.33 %
Rwork0.1802 2665 -
obs--99.9 %
Refinement TLS params.Method: refined / Details: Chain A catalytic domain / Origin x: 8.1202 Å / Origin y: -33.5248 Å / Origin z: -5.0152 Å
111213212223313233
T-0.068 Å2-0.065 Å20.0121 Å2--0.1259 Å2-0.0153 Å2---0.1428 Å2
L1.4183 °2-0.5245 °2-0.5623 °2-1.0925 °20.1851 °2--1.9705 °2
S0.0814 Å °-0.0072 Å °-0.0893 Å °0.0325 Å °-0.0147 Å °0.1181 Å °0.018 Å °0.0701 Å °-0.0666 Å °
Refinement TLS groupSelection: all

+
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