[English] 日本語
Yorodumi
- PDB-2zoq: Structural dissection of human mitogen-activated kinase ERK1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zoq
TitleStructural dissection of human mitogen-activated kinase ERK1
ComponentsMitogen-activated protein kinase 3
KeywordsTRANSFERASE / serine/threonine kinase / ERK1 / Acetylation / ATP-binding / Cell cycle / Host-virus interaction / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase
Function / homology
Function and homology information


negative regulation of cholesterol efflux / negative regulation of T cell mediated immune response to tumor cell / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis / response to epidermal growth factor / Signaling by NODAL ...negative regulation of cholesterol efflux / negative regulation of T cell mediated immune response to tumor cell / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis / response to epidermal growth factor / Signaling by NODAL / RSK activation / Signaling by MAP2K mutants / ERKs are inactivated / phosphorylation / Regulation of the apoptosome activity / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / regulation of Golgi inheritance / Signaling by LTK in cancer / peptidyl-tyrosine autophosphorylation / interleukin-1-mediated signaling pathway / positive regulation of cyclase activity / regulation of early endosome to late endosome transport / Negative feedback regulation of MAPK pathway / regulation of stress-activated MAPK cascade / positive regulation of neuroinflammatory response / IFNG signaling activates MAPKs / Frs2-mediated activation / Activation of the AP-1 family of transcription factors / MAPK3 (ERK1) activation / ERBB2-ERBB3 signaling pathway / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / positive regulation of macrophage chemotaxis / regulation of cytoskeleton organization / pseudopodium / positive regulation of telomere maintenance / ERK1 and ERK2 cascade / MAP kinase activity / BMP signaling pathway / Advanced glycosylation endproduct receptor signaling / mitogen-activated protein kinase / stress-activated MAPK cascade / Regulation of HSF1-mediated heat shock response / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate NADPH Oxidases / Signal attenuation / RHO GTPases Activate WASPs and WAVEs / Growth hormone receptor signaling / Schwann cell development / phosphatase binding / myelination / insulin-like growth factor receptor signaling pathway / NPAS4 regulates expression of target genes / sensory perception of pain / signal transduction in response to DNA damage / phosphotyrosine residue binding / Nuclear events stimulated by ALK signaling in cancer / Transcriptional and post-translational regulation of MITF-M expression and activity / negative regulation of TORC1 signaling / ESR-mediated signaling / NCAM signaling for neurite out-growth / cellular response to amino acid starvation / RNA Polymerase I Promoter Opening / Regulation of PTEN gene transcription / Signal transduction by L1 / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR3 signaling / cellular response to mechanical stimulus / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Regulation of actin dynamics for phagocytic cup formation / Oncogene Induced Senescence / Negative Regulation of CDH1 Gene Transcription / caveola / modulation of chemical synaptic transmission / insulin receptor signaling pathway / ISG15 antiviral mechanism / epidermal growth factor receptor signaling pathway / Interferon gamma signaling / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Negative regulation of MAPK pathway / MAPK cascade / Signaling by BRAF and RAF1 fusions / late endosome / nuclear envelope / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Thrombin signalling through proteinase activated receptors (PARs) / RAF/MAP kinase cascade / Senescence-Associated Secretory Phenotype (SASP)
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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
Chem-5ID / Mitogen-activated protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsKinoshita, T. / Tada, T. / Nakae, S. / Yoshida, I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal structure of human mono-phosphorylated ERK1 at Tyr204
Authors: Kinoshita, T. / Yoshida, I. / Nakae, S. / Okita, K. / Gouda, M. / Matsubara, M. / Yokota, K. / Ishiguro, H. / Tada, T.
History
DepositionJun 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / 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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase 3
B: Mitogen-activated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0788
Polymers87,0562
Non-polymers1,0226
Water5,657314
1
A: Mitogen-activated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0394
Polymers43,5281
Non-polymers5113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0394
Polymers43,5281
Non-polymers5113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.382, 91.540, 64.930
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Mitogen-activated protein kinase 3 / Extracellular signal-regulated kinase 1 / ERK-1 / Insulin-stimulated MAP2 kinase / MAP kinase 1 / ...Extracellular signal-regulated kinase 1 / ERK-1 / Insulin-stimulated MAP2 kinase / MAP kinase 1 / MAPK 1 / p44-ERK1 / ERT2 / p44-MAPK / Microtubule-associated protein 2 kinase


Mass: 43527.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK3, ERK1, PRKM3 / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P27361, mitogen-activated protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-5ID / (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL / 5-IODOTUBERCIDIN


Mass: 392.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13IN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M ammonium sulphate, 2% polyethyleneglycol400, 0.1M, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. all: 28758 / Num. obs: 28700 / % possible obs: 99.8 % / Observed criterion σ(I): 144275 / Redundancy: 5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 23.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERK

1erk
PDB Unreleased entry


Resolution: 2.39→45.57 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.267 1435 -
Rwork0.249 --
all-28700 -
obs-27265 99.8 %
Refinement stepCycle: LAST / Resolution: 2.39→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5736 0 52 314 6102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.6

+
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