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- PDB-6v6a: Inhibitory scaffolding of the ancient MAPK, ERK7 -

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Basic information

Entry
Database: PDB / ID: 6v6a
TitleInhibitory scaffolding of the ancient MAPK, ERK7
Components
  • Apical Cap Protein 9 (AC9)
  • Mitogen-activated protein kinase
KeywordsSIGNALING PROTEIN / protein kinase / MAPK / intrinsically-disordered protein / scaffold
Function / homology
Function and homology information


MAP kinase activity / mitogen-activated protein kinase / protein serine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 ...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
Mitogen-activated protein kinase / Uncharacterized protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsDewangan, P.S. / O'Shaughnessy, W.J. / Back, P.S. / Hu, X. / Bradley, P.J. / Reese, M.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1553334 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123360 United States
Welch FoundationI-1936-20170325 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Ancient MAPK ERK7 is regulated by an unusual inhibitory scaffold required forToxoplasmaapical complex biogenesis.
Authors: Back, P.S. / O'Shaughnessy, W.J. / Moon, A.S. / Dewangan, P.S. / Hu, X. / Sha, J. / Wohlschlegel, J.A. / Bradley, P.J. / Reese, M.L.
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase
B: Apical Cap Protein 9 (AC9)
C: Mitogen-activated protein kinase
D: Apical Cap Protein 9 (AC9)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8959
Polymers88,5854
Non-polymers3105
Water8,971498
1
A: Mitogen-activated protein kinase
B: Apical Cap Protein 9 (AC9)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4795
Polymers44,2922
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-9 kcal/mol
Surface area15660 Å2
MethodPISA
2
C: Mitogen-activated protein kinase
D: Apical Cap Protein 9 (AC9)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4174
Polymers44,2922
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-17 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.890, 52.938, 67.800
Angle α, β, γ (deg.)82.550, 84.580, 81.350
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Mitogen-activated protein kinase


Mass: 40717.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: MAPK2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2QDG8, mitogen-activated protein kinase
#2: Protein/peptide Apical Cap Protein 9 (AC9)


Mass: 3574.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: TGGT1_246950 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S7V0W9
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 0.15 M DL-Malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.1→29.89 Å / Num. obs: 39049 / % possible obs: 96.68 % / Redundancy: 2.4 % / Biso Wilson estimate: 17.81 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05342 / Rpim(I) all: 0.03903 / Rrim(I) all: 0.0665 / Net I/σ(I): 15.17
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.1976 / Mean I/σ(I) obs: 3.48 / Num. unique obs: 3083 / CC1/2: 0.894 / Rpim(I) all: 0.1898 / Rrim(I) all: 0.2744 / % possible all: 76.39

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
PHASER2.5.5phasing
PDB_EXTRACT3.25data extraction
CrysalisPro40.37adata reduction
CrysalisPro40.37adata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OZ6

3oz6


Resolution: 2.1→29.89 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.17
RfactorNum. reflection% reflection
Rfree0.2118 1718 4.4 %
Rwork0.1583 --
obs0.1607 39043 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.23 Å2 / Biso mean: 29.4177 Å2 / Biso min: 4.7 Å2
Refinement stepCycle: final / Resolution: 2.1→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5422 0 20 498 5940
Biso mean--44.08 31.59 -
Num. residues----682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045601
X-RAY DIFFRACTIONf_angle_d0.617565
X-RAY DIFFRACTIONf_dihedral_angle_d12.8762134
X-RAY DIFFRACTIONf_chiral_restr0.044839
X-RAY DIFFRACTIONf_plane_restr0.004970
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.160.23411100.17892406251675
2.16-2.230.24831360.17952968310492
2.23-2.310.24961290.17383142327197
2.31-2.40.21281620.16813175333799
2.4-2.510.22561460.16693179332599
2.51-2.650.23921460.162931763322100
2.65-2.810.21481550.163432243379100
2.81-3.030.24761370.165232133350100
3.03-3.330.20291460.159432123358100
3.33-3.810.19441520.140332283380100
3.81-4.80.17571500.124932053355100
4.8-29.890.20431490.17773197334699
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)
12.3674-1.30160.09492.04550.030.43740.09470.27780.0667-0.2312-0.03730.218-0.0497-0.17040.22820.12530.0642-0.01640.26950.09680.2903-7.873815.073259.6324
22.41640.94050.9542.3251-1.56462.6126-0.00310.1558-0.2143-0.19380.11690.07080.0929-0.2191-0.09260.14090.05680.01890.26780.04120.2677-12.45233.683265.2181
30.6947-0.82720.06491.5633-0.28910.08320.03440.2075-0.1245-0.02980.180.4949-0.1897-0.44010.36340.0877-0.0011-0.00020.32410.07820.2831-12.83737.061867.3945
40.5644-0.12510.26311.2379-0.52451.8230.00310.03070.10760.13360.02960.0894-0.113-0.07220.03120.09090.020.00140.09260.00790.09662.1013.81376.5292
50.7126-0.4921-0.21011.6652-0.36451.6195-0.0616-0.0019-0.1276-0.0880.03830.11110.1758-0.08240.03920.1017-0.0198-0.01750.0920.00770.07312.6033-10.88974.3152
61.7980.28750.20232.4043-0.32464.14130.07-0.1237-0.03280.04320.1646-0.45480.39660.401-0.02060.11550.03620.00540.1517-0.03420.121414.8819-14.547571.3607
72.89971.0450.89251.5949-0.46463.27120.0366-0.1126-0.47890.39570.0779-0.26910.96630.2695-0.02580.44930.0518-0.03670.18140.00350.25937.798-28.128476.611
81.32580.4572-0.08553.07730.60162.29970.0351-0.0278-0.25670.16150.0754-0.44840.26430.4095-0.00070.1580.0378-0.03440.17670.020.145114.2846-12.421983.8869
97.42831.64810.47883.8340.2844.50930.0726-0.32420.14540.36020.00710.1207-0.2043-0.0478-0.01480.19790.0328-0.00460.1535-0.00020.06133.46330.327992.5715
101.50390.04220.89781.2402-1.32423.5352-0.16630.14530.0361-0.24120.37510.6783-0.0271-1.0366-0.20050.2508-0.0324-0.03120.53040.05210.5191-19.6226-0.383771.1741
112.63960.39441.11021.69330.32444.23460.0324-0.05610.3480.1721-0.0820.0053-0.1648-0.06710.10270.18690.01980.00180.0704-0.00770.16046.701212.674675.9905
121.1276-0.16970.0176.5923-2.45193.61740.00280.14930.2727-0.4675-0.09260.3071-0.24890.0756-0.05310.14340.0186-0.01860.15390.02560.1395.2738-4.909261.9743
131.74470.0279-0.55131.6120.2271.3404-0.12680.3427-0.3564-0.35240.0277-0.25580.20670.0732-0.05840.22580.00120.06430.22-0.05020.197423.217214.94638.412
140.3875-0.03720.31331.3625-0.42592.2379-0.03910.02370.0544-0.0839-0.0151-0.0073-0.2546-0.0656-0.01690.11740.0115-0.00890.1331-0.00540.096213.266135.121445.8945
151.83670.203-1.30561.9430.16195.3949-0.02130.0746-0.4265-0.2864-0.0469-0.07840.31140.05550.07290.20070.01010.00880.1226-0.00640.224313.238310.146348.8747
162.94181.4044-0.16290.9937-1.22674.0935-0.02150.3137-0.2939-0.39370.0220.0650.51170.096-0.67520.26970.0208-0.06390.2448-0.07560.097611.921723.212230.3962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 32 )A4 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 67 )A33 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 87 )A68 - 87
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 152 )A88 - 152
5X-RAY DIFFRACTION5chain 'A' and (resid 153 through 216 )A153 - 216
6X-RAY DIFFRACTION6chain 'A' and (resid 217 through 237 )A217 - 237
7X-RAY DIFFRACTION7chain 'A' and (resid 238 through 259 )A238 - 259
8X-RAY DIFFRACTION8chain 'A' and (resid 260 through 296 )A260 - 296
9X-RAY DIFFRACTION9chain 'A' and (resid 297 through 314 )A297 - 314
10X-RAY DIFFRACTION10chain 'A' and (resid 315 through 349 )A315 - 349
11X-RAY DIFFRACTION11chain 'B' and (resid 420 through 440 )B420 - 440
12X-RAY DIFFRACTION12chain 'B' and (resid 441 through 452 )B441 - 452
13X-RAY DIFFRACTION13chain 'C' and (resid 5 through 177 )C5 - 177
14X-RAY DIFFRACTION14chain 'C' and (resid 178 through 324 )C178 - 324
15X-RAY DIFFRACTION15chain 'D' and (resid 420 through 440 )D420 - 440
16X-RAY DIFFRACTION16chain 'D' and (resid 441 through 452 )D441 - 452

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