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- PDB-4ic7: Crystal structure of the ERK5 kinase domain in complex with an MK... -

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Basic information

Entry
Database: PDB / ID: 4ic7
TitleCrystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment
Components
  • Dual specificity mitogen-activated protein kinase kinase 5
  • Mitogen-activated protein kinase 7
KeywordsTRANSFERASE / kinase domain / SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


ERK5 cascade / negative regulation of chemokine (C-X-C motif) ligand 2 production / 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 / negative regulation of interleukin-8 production / mitogen-activated protein kinase kinase ...ERK5 cascade / negative regulation of chemokine (C-X-C motif) ligand 2 production / 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 / negative regulation of interleukin-8 production / mitogen-activated protein kinase kinase / cellular response to laminar fluid shear stress / Gastrin-CREB signalling pathway via PKC and MAPK / negative regulation of cell migration involved in sprouting angiogenesis / ERKs are inactivated / mitogen-activated protein kinase binding / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of NF-kappaB transcription factor activity / ERK/MAPK targets / MAP kinase kinase activity / 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 / insulin-like growth factor receptor signaling pathway / positive regulation of epithelial cell proliferation / positive regulation of MAP kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / spindle / cellular response to hydrogen peroxide / cellular response to growth factor stimulus / negative regulation of inflammatory response / MAPK cascade / heart development / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / protein tyrosine kinase activity / cell differentiation / protein kinase activity / intracellular signal transduction / cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Dual specificity mitogen-activated protein kinase kinase 5, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Transferase(Phosphotransferase) domain 1 ...Dual specificity mitogen-activated protein kinase kinase 5, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / 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 / Roll / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Dual specificity mitogen-activated protein kinase kinase 5 / Mitogen-activated protein kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGogl, G. / Remenyi, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural mechanism for the specific assembly and activation of the extracellular signal regulated kinase 5 (ERK5) module.
Authors: Glatz, G. / Gogl, G. / Alexa, A. / Remenyi, A.
History
DepositionDec 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 7
D: Mitogen-activated protein kinase 7
E: Dual specificity mitogen-activated protein kinase kinase 5
B: Dual specificity mitogen-activated protein kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9946
Polymers127,9824
Non-polymers1,0122
Water1,49583
1
A: Mitogen-activated protein kinase 7
B: Dual specificity mitogen-activated protein kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4973
Polymers63,9912
Non-polymers5061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-7 kcal/mol
Surface area22500 Å2
MethodPISA
2
D: Mitogen-activated protein kinase 7
E: Dual specificity mitogen-activated protein kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4973
Polymers63,9912
Non-polymers5061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-9 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.370, 69.370, 271.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 49802.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK7, BMK1, ERK5, PRKM7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13164, mitogen-activated protein kinase
#2: Protein Dual specificity mitogen-activated protein kinase kinase 5 / MAP kinase kinase 5 / MAPKK 5 / MAPK/ERK kinase 5 / MEK 5


Mass: 14187.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K5, MEK5, MKK5, PRKMK5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13163, mitogen-activated protein kinase kinase
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 48% PEG 200, 100mM MIB, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 31, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.27 Å / Num. all: 39260 / Num. obs: 39147 / % possible obs: 99.7 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 4.5 % / % possible all: 98.62

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.269 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 32.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 1955 5.01 %
Rwork0.2106 --
obs0.213 39029 99.62 %
all-39260 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7249 0 62 83 7394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087486
X-RAY DIFFRACTIONf_angle_d1.58410209
X-RAY DIFFRACTIONf_dihedral_angle_d18.9982763
X-RAY DIFFRACTIONf_chiral_restr0.1171148
X-RAY DIFFRACTIONf_plane_restr0.0111327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6650.40011350.31242624X-RAY DIFFRACTION98
2.665-2.73710.33221380.29922622X-RAY DIFFRACTION99
2.7371-2.81760.37581460.28682631X-RAY DIFFRACTION99
2.8176-2.90850.36481480.28112615X-RAY DIFFRACTION100
2.9085-3.01250.33241530.26912658X-RAY DIFFRACTION100
3.0125-3.13310.3631360.2632636X-RAY DIFFRACTION100
3.1331-3.27560.30121200.26922691X-RAY DIFFRACTION100
3.2756-3.44830.25761280.23572659X-RAY DIFFRACTION100
3.4483-3.66420.28381340.2212670X-RAY DIFFRACTION100
3.6642-3.9470.26031450.2112622X-RAY DIFFRACTION100
3.947-4.3440.24751570.18512665X-RAY DIFFRACTION100
4.344-4.97210.19131370.16992653X-RAY DIFFRACTION100
4.9721-6.26210.251350.19952661X-RAY DIFFRACTION100
6.2621-48.27730.20221430.17132667X-RAY DIFFRACTION100

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