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- PDB-4ic8: Crystal structure of the apo ERK5 kinase domain -

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Basic information

Entry
Database: PDB / ID: 4ic8
TitleCrystal structure of the apo ERK5 kinase domain
ComponentsMitogen-activated protein kinase 7
KeywordsTRANSFERASE / KINASE / SIGNALING
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 / 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 ...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 / 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 / negative regulation of smooth muscle cell apoptotic process / 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
Mitogen-activated protein kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
B: Mitogen-activated protein kinase 7


Theoretical massNumber of molelcules
Total (without water)99,6062
Polymers99,6062
Non-polymers00
Water0
1
A: Mitogen-activated protein kinase 7


Theoretical massNumber of molelcules
Total (without water)49,8031
Polymers49,8031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 7


Theoretical massNumber of molelcules
Total (without water)49,8031
Polymers49,8031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 93.220, 69.260
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211

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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

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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: 1.94 Å3/Da / Density % sol: 36.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% PEG 200, 100mM MIB, pH 4.5, 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: 2.8→45.29 Å / Num. all: 18893 / Num. obs: 18522 / % possible obs: 98 % / Observed criterion σ(F): 2.52 / Observed criterion σ(I): 2.52
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.3 % / % possible all: 100

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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: 2.8→45.29 Å / σ(F): 1.34 / Phase error: 32.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 953 5.14 %RANDOM
Rwork0.2619 ---
all0.2632 18893 --
obs0.2632 18522 98.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→45.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 0 0 4807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064920
X-RAY DIFFRACTIONf_angle_d1.5196731
X-RAY DIFFRACTIONf_dihedral_angle_d18.0411660
X-RAY DIFFRACTIONf_chiral_restr0.098783
X-RAY DIFFRACTIONf_plane_restr0.007881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94850.34611380.32542555X-RAY DIFFRACTION95
2.9485-3.13320.3671320.32522556X-RAY DIFFRACTION95
3.1332-3.3750.34251360.30122542X-RAY DIFFRACTION95
3.375-3.71440.28541310.27382543X-RAY DIFFRACTION95
3.7144-4.25140.29181300.25172197X-RAY DIFFRACTION82
4.2514-5.35440.26421530.23132562X-RAY DIFFRACTION94
5.3544-40.76430.26361280.24112605X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82070.42870.27880.2680.08540.2051-0.31210.6491-0.3715-0.1296-0.0631-0.35870.2049-0.058-0.19970.26380.13140.41170.85060.00581.088833.2808-44.23095.0999
25.14080.0844-0.20371.01011.74763.01690.2104-0.1311-0.27440.1845-0.0967-0.4289-0.0941-0.4285-0.06290.29290.07790.07570.35060.07630.767233.2631-35.54067.9493
31.275-0.519-0.16382.38050.32431.9044-0.3187-0.1459-0.1708-0.22980.2147-0.3851-0.21670.3036-0.00420.61730.0557-0.01540.40920.00920.377331.2668-30.031913.0794
43.741-0.0011.53131.74580.81251.37580.3135-0.1061-0.49360.3571-0.1102-0.6658-0.4253-0.0033-0.01340.5492-0.0383-0.03440.3526-0.03660.367920.7634-22.409318.1961
51.3728-0.1402-0.17780.8881-1.35013.0245-0.1970.1090.2929-0.22330.00760.29390.0923-0.06760.06430.82590.00990.08050.35670.01820.356112.7491-10.815213.1483
63.3508-0.1679-1.27210.4793-0.54053.18340.19280.19070.2488-0.67160.37540.4243-0.1541-0.6310.21040.72560.0291-0.03840.36990.17310.84259.32284.421114.4101
77.09020.82990.99960.76250.70140.7413-0.67840.20350.75130.03420.54870.4632-0.3787-0.32050.04260.5807-0.0750.01110.82530.05940.42664.1369-13.56226.278
83.66750.21580.41731.31731.40681.63860.3423-0.3282-0.18871.32740.5214-0.1501-0.66640.0955-0.07980.70250.0095-0.03360.63390.0220.302516.0317-11.3127.5665
90.3188-0.7172-0.04412.65760.22760.02370.126-0.12770.01130.79650.4143-0.87190.17940.31410.11910.7059-0.0938-0.24511.1428-0.07010.362233.9492-18.555724.2105
102.2255-0.0541-0.01860.8350.51921.4998-0.0913-0.25880.10140.16190.2339-0.51640.08870.61770.29680.14870.1452-0.08080.85370.07150.967546.384-26.12467.7732
112.0581-0.7420.78431.6471-0.35751.0801-0.10550.36890.67630.07770.10490.2471-0.6640.0813-0.13650.5051-0.35120.06820.29040.17270.7548-2.4296-5.4127-30.8904
121.95512.49581.04114.7314-0.01531.7721-0.3016-0.1828-0.0553-0.41650.1960.6818-0.6033-0.34050.06240.37730.1299-0.0250.41210.14230.582-4.5258-16.115-26.4373
132.44991.06030.54573.38780.31122.6663-0.3210.0385-0.2139-0.10650.38160.864-1.03760.13460.03610.64430.24610.17970.33410.09540.5444-7.2385-15.3378-20.1966
144.5782-0.19561.99622.0167-0.19273.36190.0714-0.16520.6589-0.4697-0.00360.131-1.10250.01510.1420.6739-0.11990.08090.20320.05880.39567.7882-14.9124-22.6672
151.960.0163-0.68431.10170.38671.16990.04250.0347-0.1158-0.3782-0.00810.06630.03590.17760.08010.46960.0296-0.03570.50230.06770.338912.7879-30.1453-18.5116
162.4736-2.3133-2.73963.74261.31694.5361-0.09130.1576-0.58820.76180.20930.45750.2960.84710.15710.90.05860.09630.4573-0.09990.803319.541-52.0189-20.0295
172.9053-1.28370.50290.74070.08850.8433-0.4151-0.5969-0.7230.78980.09250.17950.20820.3008-0.15420.68610.2454-0.38410.61150.13530.356713.6493-32.3525-6.72
184.2116-0.74611.09544.7626-2.73051.65840.06170.21560.02330.0173-0.35160.6566-0.1823-0.75440.10420.5632-0.064-0.16310.660.07440.5617-15.9945-24.2976-27.4969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 135 )
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 206 )
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 256 )
6X-RAY DIFFRACTION6chain 'A' and (resid 257 through 286 )
7X-RAY DIFFRACTION7chain 'A' and (resid 287 through 305 )
8X-RAY DIFFRACTION8chain 'A' and (resid 306 through 328 )
9X-RAY DIFFRACTION9chain 'A' and (resid 329 through 350 )
10X-RAY DIFFRACTION10chain 'A' and (resid 351 through 368 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 45 )
12X-RAY DIFFRACTION12chain 'B' and (resid 46 through 86 )
13X-RAY DIFFRACTION13chain 'B' and (resid 87 through 106 )
14X-RAY DIFFRACTION14chain 'B' and (resid 107 through 133 )
15X-RAY DIFFRACTION15chain 'B' and (resid 134 through 256 )
16X-RAY DIFFRACTION16chain 'B' and (resid 257 through 286 )
17X-RAY DIFFRACTION17chain 'B' and (resid 287 through 343 )
18X-RAY DIFFRACTION18chain 'B' and (resid 344 through 368 )

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