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- PDB-1cm8: PHOSPHORYLATED MAP KINASE P38-GAMMA -

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Basic information

Entry
Database: PDB / ID: 1cm8
TitlePHOSPHORYLATED MAP KINASE P38-GAMMA
ComponentsPHOSPHORYLATED MAP KINASE P38-GAMMA
KeywordsTRANSFERASE / P38-GAMMA / GAMMA / PHOSPHORYLATION / MAP KINASE
Function / homology
Function and homology information


myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / peptidase activator activity / muscle organ development / positive regulation of muscle cell differentiation / Myogenesis / negative regulation of cell cycle / signal transduction in response to DNA damage / MAP kinase activity / mitogen-activated protein kinase ...myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / peptidase activator activity / muscle organ development / positive regulation of muscle cell differentiation / Myogenesis / negative regulation of cell cycle / signal transduction in response to DNA damage / MAP kinase activity / mitogen-activated protein kinase / p38MAPK events / NOD1/2 Signaling Pathway / VEGFA-VEGFR2 Pathway / Negative regulation of MAPK pathway / MAPK cascade / regulation of cell cycle / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein kinase 12 / Mitogen-activated protein (MAP) kinase p38-like / 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 / Protein kinase domain ...Mitogen-activated protein kinase 12 / Mitogen-activated protein (MAP) kinase p38-like / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsBellon, S. / Fitzgibbon, M.J. / Fox, T. / Hsiao, H.M. / Wilson, K.P.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The structure of phosphorylated p38gamma is monomeric and reveals a conserved activation-loop conformation.
Authors: Bellon, S. / Fitzgibbon, M.J. / Fox, T. / Hsiao, H.M. / Wilson, K.P.
History
DepositionMay 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORYLATED MAP KINASE P38-GAMMA
B: PHOSPHORYLATED MAP KINASE P38-GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4248
Polymers84,3142
Non-polymers1,1106
Water3,351186
1
A: PHOSPHORYLATED MAP KINASE P38-GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7124
Polymers42,1571
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHORYLATED MAP KINASE P38-GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7124
Polymers42,1571
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.500, 66.820, 206.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0105, -0.9989, -0.0454), (-0.9999, 0.0108, -0.0073), (0.0077, 0.0454, -0.9989)
Vector: 83.9047, 79.1746, 47.9239)

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Components

#1: Protein PHOSPHORYLATED MAP KINASE P38-GAMMA / STRESS-ACTIVATED PROTEIN KINASE-3 / ERK6 / ERK5


Mass: 42157.090 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: P53778
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#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


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.5 mMprotein1drop
25 mMAMP-PNP1drop
30.02 %1dropC12E9
4100 mM1reservoirNaOAc
5100 mMTris1reservoirpH8.5
627 %PEG40001reservoir
710 mM1reservoirMgCl2
85 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 31732 / % possible obs: 89.9 % / Redundancy: 3.7 % / Rsym value: 6.7 / Net I/σ(I): 9.8
Reflection
*PLUS
Num. measured all: 118429 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / % possible obs: 76.5 %

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Processing

Software
NameVersionClassification
CNS0.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→50 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE DATA ARE EXTREMELY ANISOTROPIC. THIS RESULTED IN LESS THAN 100% COMPLETENESS FOR THE NATIVE DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 2768 9.9 %RANDOM
Rwork0.2322 ---
obs-27840 79.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5190 0 66 186 5442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: CNS / Version: 0.2 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6

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