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- PDB-6una: Crystal structure of inactive p38gamma -

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Basic information

Entry
Database: PDB / ID: 6una
TitleCrystal structure of inactive p38gamma
ComponentsMitogen-activated protein kinase 12P38 mitogen-activated protein kinases
KeywordsTRANSFERASE / MAPK / mitogen activated protein kinase / p38 gamma / MAPK12 / inactive kinase
Function / homology
Function and homology information


positive regulation of peptidase activity / myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / muscle organ development / DSCAM interactions / positive regulation of muscle cell differentiation / Myogenesis / negative regulation of cell cycle / MAP kinase activity / mitogen-activated protein kinase ...positive regulation of peptidase activity / myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / muscle organ development / DSCAM interactions / positive regulation of muscle cell differentiation / Myogenesis / negative regulation of cell cycle / MAP kinase activity / mitogen-activated protein kinase / signal transduction in response to DNA damage / p38MAPK events / NOD1/2 Signaling Pathway / VEGFA-VEGFR2 Pathway / Negative regulation of MAPK pathway / MAPK cascade / peptidyl-serine phosphorylation / regulation of cell cycle / intracellular signal transduction / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
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. / 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
Similarity search - Domain/homology
Mitogen-activated protein kinase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.554 Å
AuthorsAoto, P.C. / Stanfield, R.L. / Wilson, I.A. / Dyson, H.J. / Wright, P.E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM75995 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Biochemistry / Year: 2019
Title: A Dynamic Switch in Inactive p38 gamma Leads to an Excited State on the Pathway to an Active Kinase.
Authors: Aoto, P.C. / Stanfield, R.L. / Wilson, I.A. / Dyson, H.J. / Wright, P.E.
History
DepositionOct 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 12
B: Mitogen-activated protein kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2356
Polymers82,8592
Non-polymers3764
Water81145
1
A: Mitogen-activated protein kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6183
Polymers41,4301
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6183
Polymers41,4301
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.032, 66.359, 68.568
Angle α, β, γ (deg.)115.270, 102.490, 96.830
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 69 or resid 71...
21(chain B and (resid 10 through 69 or resid 71...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYS(chain A and (resid 10 through 69 or resid 71...AA10 - 694 - 63
12ALAALALEULEU(chain A and (resid 10 through 69 or resid 71...AA71 - 17065 - 164
13PHEPHEGLYGLY(chain A and (resid 10 through 69 or resid 71...AA172 - 173166 - 167
14GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
15GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
16GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
17GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
18GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
19GLYGLYPHEPHE(chain A and (resid 10 through 69 or resid 71...AA10 - 3514 - 345
21GLYGLYLYSLYS(chain B and (resid 10 through 69 or resid 71...BB10 - 694 - 63
22ALAALALEULEU(chain B and (resid 10 through 69 or resid 71...BB71 - 17065 - 164
23PHEPHEGLUGLU(chain B and (resid 10 through 69 or resid 71...BB172 - 318166 - 312
24PROPROPHEPHE(chain B and (resid 10 through 69 or resid 71...BB321 - 351315 - 345

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Components

#1: Protein Mitogen-activated protein kinase 12 / P38 mitogen-activated protein kinases / MAPK 12 / Extracellular signal-regulated kinase 6 / ERK-6 / Mitogen-activated protein kinase p38 ...MAPK 12 / Extracellular signal-regulated kinase 6 / ERK-6 / Mitogen-activated protein kinase p38 gamma / MAP kinase p38 gamma / Stress-activated protein kinase 3


Mass: 41429.500 Da / Num. of mol.: 2 / Mutation: Q31R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK12, ERK6, SAPK3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: P53778, mitogen-activated protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.7 / Details: 2.4M Ammonium sulfate, 50mM TRIS pH 7.7.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03316 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 2.55→44.585 Å / Num. obs: 22388 / % possible obs: 98.1 % / Redundancy: 1.9 % / Biso Wilson estimate: 42.33 Å2 / CC1/2: 0.91 / Rpim(I) all: 0.075 / Rrim(I) all: 0.11 / Rsym value: 0.075 / Net I/σ(I): 10.3
Reflection shellResolution: 2.55→2.62 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1051 / CC1/2: 0.68 / Rpim(I) all: 0.37 / Rrim(I) all: 0.53 / Rsym value: 0.37

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cm8

1cm8


Resolution: 2.554→44.585 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.38
RfactorNum. reflection% reflection
Rfree0.2455 1112 4.97 %
Rwork0.1953 --
obs0.1978 22386 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.81 Å2 / Biso mean: 50.366 Å2 / Biso min: 19.69 Å2
Refinement stepCycle: final / Resolution: 2.554→44.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5339 0 22 45 5406
Biso mean--76.42 38.19 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035488
X-RAY DIFFRACTIONf_angle_d0.5847410
X-RAY DIFFRACTIONf_chiral_restr0.041811
X-RAY DIFFRACTIONf_plane_restr0.004944
X-RAY DIFFRACTIONf_dihedral_angle_d9.7523302
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3128X-RAY DIFFRACTION9.164TORSIONAL
12B3128X-RAY DIFFRACTION9.164TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.554-2.67020.34221230.2743241388
2.6702-2.8110.30951490.2456266898
2.811-2.98710.27361350.2464269998
2.9871-3.21770.31481370.2395266698
3.2177-3.54140.2751470.2026270498
3.5414-4.05350.22191400.1718269998
4.0535-5.10580.19131390.1553271099
5.1058-44.5850.22561420.1827271599
Refinement TLS params.Method: refined / Origin x: 16.2644 Å / Origin y: 7.1797 Å / Origin z: -38.1372 Å
111213212223313233
T0.1935 Å2-0.0011 Å2-0.0017 Å2-0.2159 Å20.0293 Å2--0.2815 Å2
L0.4255 °20.0114 °20.0494 °2-0.549 °20.498 °2--1.3625 °2
S0.0763 Å °0.03 Å °-0.0448 Å °0.0466 Å °-0.0054 Å °-0.0016 Å °0.0739 Å °-0.0287 Å °-0.0699 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 351
2X-RAY DIFFRACTION1allB9 - 351
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD2 - 4
5X-RAY DIFFRACTION1allS1 - 79

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