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- PDB-7ugb: Crystal structure of rat ERK2 complexed with docking peptide from... -

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Basic information

Entry
Database: PDB / ID: 7ugb
TitleCrystal structure of rat ERK2 complexed with docking peptide from ISG20
Components
  • Interferon-stimulated gene 20 kDa protein
  • Mitogen-activated protein kinase 1
KeywordsSIGNALING PROTEIN / kinase / complex / docking
Function / homology
Function and homology information


exoribonuclease II / exoribonuclease II activity / phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors ...exoribonuclease II / exoribonuclease II activity / phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of actin dynamics for phagocytic cup formation / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Signaling by Activin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of the apoptosome activity / Signal transduction by L1 / Negative regulation of FGFR2 signaling / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / Interferon gamma signaling / FCERI mediated MAPK activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / diadenosine tetraphosphate biosynthetic process / Recycling pathway of L1 / neural crest cell development / single-stranded DNA 3'-5' DNA exonuclease activity / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / mitogen-activated protein kinase kinase kinase binding / regulation of cellular pH / DNA catabolic process / positive regulation of macrophage proliferation / outer ear morphogenesis / RNA catabolic process / Thrombin signalling through proteinase activated receptors (PARs) / RAF/MAP kinase cascade / regulation of Golgi inheritance / ERBB signaling pathway / U3 snoRNA binding / labyrinthine layer blood vessel development / Neutrophil degranulation / mammary gland epithelial cell proliferation / exonuclease activity / trachea formation / regulation of early endosome to late endosome transport / : / regulation of stress-activated MAPK cascade / negative regulation of viral genome replication / positive regulation of macrophage chemotaxis / lung morphogenesis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / androgen receptor signaling pathway / pseudopodium / progesterone receptor signaling pathway / negative regulation of cell differentiation / Bergmann glial cell differentiation / positive regulation of telomere capping / thyroid gland development / decidualization / steroid hormone mediated signaling pathway / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / phosphatase binding / U2 snRNA binding / Cajal body / Schwann cell development / stress-activated MAPK cascade / U1 snRNA binding / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / sensory perception of pain / cellular response to cadmium ion / positive regulation of telomere maintenance via telomerase / ERK1 and ERK2 cascade / cellular response to amino acid starvation
Similarity search - Function
: / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Serine/threonine-protein kinase, active site ...: / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase 1 / Interferon-stimulated gene 20 kDa protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsTorres Robles, J. / Stiegler, A.L. / Boggon, T.J. / Turk, B.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM135331 United States
National Science Foundation (NSF, United States)1752134 United States
CitationJournal: To Be Published
Title: To be determined
Authors: Torres Robles, J. / Turk, B.E.
History
DepositionMar 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 1
I: Interferon-stimulated gene 20 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8363
Polymers45,3302
Non-polymers5061
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-6 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.888, 66.679, 116.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: 43720.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Unphosphorylated / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mapk1, Erk2, Mapk, Prkm1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P63086, mitogen-activated protein kinase
#2: Protein/peptide Interferon-stimulated gene 20 kDa protein / Estrogen-regulated transcript 45 protein / Promyelocytic leukemia nuclear body-associated protein ISG20


Mass: 1609.920 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96AZ6, exoribonuclease II
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 % PEG 4000, 0.1 M HEPES [pH 7.5] and 5 % Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 29145 / % possible obs: 100 % / Redundancy: 23.7 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.026 / Rrim(I) all: 0.13 / Χ2: 0.933 / Net I/σ(I): 6.6 / Num. measured all: 692189
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.9-1.9715.41.24428660.8280.3081.2840.63
1.97-2.0518.70.99628300.9330.2291.0220.667
2.05-2.1421.70.75328760.9520.1620.770.729
2.14-2.2525.10.59928750.9810.1210.6110.809
2.25-2.3926.90.45728900.9890.0890.4660.879
2.39-2.5826.70.33228880.9920.0650.3381.02
2.58-2.8425.90.22129010.9960.0440.2261.065
2.84-3.2524.80.14329350.9970.0290.1461.096
3.25-4.0927.50.09529520.9990.0180.0971.079
4.09-5024.50.06931320.9990.0140.071.093

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.31 Å43.97 Å
Translation5.31 Å43.97 Å

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Processing

Software
NameVersionClassification
HKL-2000721.2data scaling
PHASER2.8.3phasing
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
HKL-2000721.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FMQ

4fmq


Resolution: 1.9→43.97 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 1451 5 %
Rwork0.1792 27569 -
obs0.1815 29020 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.12 Å2 / Biso mean: 47.4003 Å2 / Biso min: 21.01 Å2
Refinement stepCycle: final / Resolution: 1.9→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 31 146 3012
Biso mean--49.71 45.26 -
Num. residues----348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.970.27131380.23772686282499
1.97-2.050.27261490.228526782827100
2.05-2.140.26241360.209527402876100
2.14-2.250.24481510.193227192870100
2.25-2.390.24191610.227242885100
2.39-2.580.25121590.199127162875100
2.58-2.840.26251340.200627592893100
2.84-3.250.23621310.193427972928100
3.25-4.090.2091400.15727992939100
4.09-43.970.20261520.159429513103100
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)
15.93470.28980.77263.6106-1.4793.5021-0.1591-0.67341.2634-0.3147-0.34570.4659-1.1337-0.48670.3710.6610.1422-0.13590.504-0.17410.5848-19.1331-0.90167.8408
27.34861.92960.57967.6873-2.36144.86830.07610.15930.1598-0.343-0.2475-0.2783-0.51210.31640.36330.39820.03170.03760.2766-0.0090.2336-5.8679-11.965710.4389
31.6926-0.35260.57533.3124-0.53663.2360.00990.12080.1433-0.2074-0.08780.1331-0.3114-0.02540.050.2210.0164-0.00910.1979-0.03390.2685-12.5352-13.106217.5699
45.72691.59371.61032.84580.47581.49090.1448-0.3618-0.04860.2154-0.1102-0.13480.01980.0888-0.04570.2331-0.0070.02570.24160.0160.2131-1.0738-16.468137.0133
52.46170.5654-0.72348.0146-3.1299.07520.02730.0916-0.48310.00230.01960.27361.26-0.1317-0.07750.36180.0011-0.04240.1824-0.010.3832-12.271-32.862125.0651
61.23450.8565-1.09518.1696-5.00636.2730.10170.253-0.0351-0.7675-0.577-1.1692-0.12380.74390.35030.4574-0.00380.08020.54020.00130.3844-0.6677-10.40094.0154
73.7333-4.041-5.93934.30176.41819.354-0.12480.8073-1.1439-0.1221-0.73752.43820.2415-1.9510.76030.4639-0.0181-0.02460.6188-0.06711.0035-26.738-27.340321.0526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 61 )A11 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 85 )A62 - 85
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 189 )A86 - 189
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 303 )A190 - 303
5X-RAY DIFFRACTION5chain 'A' and (resid 304 through 321 )A304 - 321
6X-RAY DIFFRACTION6chain 'A' and (resid 322 through 356 )A322 - 356
7X-RAY DIFFRACTION7chain 'I' and (resid 168 through 181 )I168 - 181

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