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- PDB-7opm: Phosphorylated ERK2 in complex with ORF45 -

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Basic information

Entry
Database: PDB / ID: 7opm
TitlePhosphorylated ERK2 in complex with ORF45
Components
  • Mitogen-activated protein kinase 1
  • Protein ORF45
  • synthetic ERK2 inhibitor peptide
KeywordsVIRAL PROTEIN / MAPK / ERK2 / phosphorylated ERK2 / ORF45 / kaposi's sarcoma-associated herpesvirus / FXFP-motif
Function / homology
Function and homology information


symbiont-mediated perturbation of host innate immune response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / viral tegument / phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development ...symbiont-mediated perturbation of host innate immune response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / viral tegument / phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / ERKs are inactivated / cytosine metabolic process / response to epidermal growth factor / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / Regulation of the apoptosome activity / outer ear morphogenesis / regulation of cellular pH / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / positive regulation of macrophage chemotaxis / lung morphogenesis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / progesterone receptor signaling pathway / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / pseudopodium / Recycling pathway of L1 / MAPK1 (ERK2) activation / Bergmann glial cell differentiation / negative regulation of cell differentiation / positive regulation of telomere capping / thyroid gland development / Advanced glycosylation endproduct receptor signaling / steroid hormone receptor signaling pathway / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate NADPH Oxidases / Regulation of HSF1-mediated heat shock response / MAP kinase activity / regulation of ossification / RHO GTPases Activate WASPs and WAVEs / phosphatase binding / mitogen-activated protein kinase / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Nuclear events stimulated by ALK signaling in cancer / Schwann cell development / Growth hormone receptor signaling / stress-activated MAPK cascade / lipopolysaccharide-mediated signaling pathway / : / positive regulation of telomere maintenance via telomerase / cellular response to cadmium ion / NPAS4 regulates expression of target genes / ERK1 and ERK2 cascade / myelination / cellular response to amino acid starvation / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription / Signal transduction by L1 / caveola / long-term synaptic potentiation / Negative regulation of FGFR3 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / FCERI mediated MAPK activation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / FCGR3A-mediated phagocytosis / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / peptidyl-threonine phosphorylation / B cell receptor signaling pathway / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / response to nicotine / MAP2K and MAPK activation / regulation of protein stability
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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
Similarity search - Domain/homology
Chem-08G / Protein ORF45 / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
Human herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsSok, P. / Remenyi, A. / Alexa, A. / Poti, A.
Funding support Hungary, European Union, 2items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)KKP 126963 Hungary
European Union (EU)iNEXT Project 4788European Union
CitationJournal: Nat Commun / Year: 2022
Title: A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host.
Authors: Alexa, A. / Sok, P. / Gross, F. / Albert, K. / Kobori, E. / Poti, A.L. / Gogl, G. / Bento, I. / Kuang, E. / Taylor, S.S. / Zhu, F. / Ciliberto, A. / Remenyi, A.
History
DepositionJun 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 12, 2022Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 1
B: synthetic ERK2 inhibitor peptide
C: Protein ORF45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3657
Polymers45,7783
Non-polymers5884
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-21 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.094, 41.149, 51.701
Angle α, β, γ (deg.)90.000, 92.350, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mitogen-activated protein kinase 1 / MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform ...MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAP kinase 2 / MAPK 2


Mass: 41906.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P28482, mitogen-activated protein kinase

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Protein/peptide , 2 types, 2 molecules BC

#2: Protein/peptide synthetic ERK2 inhibitor peptide / p28


Mass: 2276.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Protein ORF45


Mass: 1593.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 8 / References: UniProt: F5HDE4

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Non-polymers , 3 types, 43 molecules

#4: Chemical ChemComp-08G / 1-[4-(hydroxymethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-3-[(1S)-1-phenylethyl]urea


Mass: 311.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N5O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.44 Å3/Da / Density % sol: 49.57 % / Description: thick needles grown in clusters
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1M Tris pH 8.3, 20% PEG 8000 with 1.25 M NaCl in reservoir
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.45→47.12 Å / Num. obs: 16460 / % possible obs: 99.3 % / Redundancy: 8.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.045 / Rrim(I) all: 0.131 / Net I/σ(I): 10.1 / Num. measured all: 140097
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.45-2.558.41.3071536118290.7490.4781.3951.599
8.83-47.128.30.07131053740.9970.0250.07528.796.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ERK

2erk


Resolution: 2.45→47.12 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 1632 9.94 %
Rwork0.2352 14781 -
obs0.237 16413 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.17 Å2 / Biso mean: 77.717 Å2 / Biso min: 29.57 Å2
Refinement stepCycle: final / Resolution: 2.45→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 41 39 3193
Biso mean--66.83 68.98 -
Num. residues----391
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 (%)
2.45-2.520.37721280.34721192132099
2.52-2.60.40881370.33581230136799
2.6-2.70.37041350.341112121347100
2.7-2.80.35331400.327812281368100
2.8-2.930.35581420.31331229137199
2.93-3.090.3471300.30191226135699
3.09-3.280.26071320.26971229136199
3.28-3.530.23771390.25021218135798
3.53-3.890.2391320.21831241137399
3.89-4.450.20851400.19671235137599
4.45-5.610.25371360.19461253138999
5.61-47.120.18521410.19651288142998
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)
19.07360.2215.12560.5441.4256.15670.20740.9209-0.5576-0.3022-0.083-0.34680.52210.72240.05080.8856-0.0065-0.06550.2891-0.0010.510752.22-11.74418.265
24.7808-0.20980.32691.26940.01932.6347-0.0480.3413-0.2776-0.0851-0.11330.2968-0.105-1.22550.14780.56210.0508-0.02610.7569-0.11820.378227.051-4.00216.179
33.9276-0.6833-1.08221.34990.44323.84810.01590.19810.3909-0.0464-0.04490.2648-0.7334-1.2103-0.03240.69660.1467-0.11420.8713-0.04860.381426.4933.86519.083
44.7906-3.50861.14169.6768-7.11425.8129-1.46810.9453-0.4513-2.00111.48321.1960.7818-1.9634-0.03751.2539-0.245-0.13741.8755-0.31970.913515.037-13.089-2.2
55.25092.1689-1.41271.03-1.4055.4345-0.5974-1.5884-0.73850.83530.46340.03390.9586-0.06880.26721.09030.30010.08391.14060.01230.514131.53-6.31340.606
65.59290.2668-1.73344.44762.73178.8698-0.2818-1.59960.61930.54470.28780.1816-0.5182-0.4024-0.03520.99790.1228-0.06271.0075-0.20780.603829.4816.49541.493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:44 )A-1 - 44
2X-RAY DIFFRACTION2( CHAIN A AND RESID 45:274 )A45 - 274
3X-RAY DIFFRACTION3( CHAIN A AND RESID 275:360 )A275 - 360
4X-RAY DIFFRACTION4( CHAIN C AND RESID 30:39 )C30 - 39
5X-RAY DIFFRACTION5( CHAIN B AND RESID 3:10 )B3 - 10
6X-RAY DIFFRACTION6( CHAIN B AND RESID 11:20 )B11 - 20

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