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- PDB-6f5e: Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_1... -

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Basic information

Entry
Database: PDB / ID: 6f5e
TitleCrystal structure of DARPin-DARPin rigid fusion, variant DD_D12_10_47 in complex JNK1a1 and JIP1 peptide
Components
  • C-Jun-amino-terminal kinase-interacting protein 1
  • DD_D12_10_47
  • Mitogen-activated protein kinase 8
KeywordsDE NOVO PROTEIN / X-ray crystallography / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions / transferase
Function / homology
Function and homology information


positive regulation of cell killing / dentate gyrus mossy fiber / JUN phosphorylation / regulation of CD8-positive, alpha-beta T cell proliferation / regulation of DNA replication origin binding / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity ...positive regulation of cell killing / dentate gyrus mossy fiber / JUN phosphorylation / regulation of CD8-positive, alpha-beta T cell proliferation / regulation of DNA replication origin binding / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / protein serine/threonine kinase binding / negative regulation of JNK cascade / JUN kinase binding / mitogen-activated protein kinase kinase kinase binding / positive regulation of cyclase activity / histone deacetylase regulator activity / mitogen-activated protein kinase kinase binding / positive regulation of NLRP3 inflammasome complex assembly / DSCAM interactions / NRAGE signals death through JNK / Activation of the AP-1 family of transcription factors / dendritic growth cone / Fc-epsilon receptor signaling pathway / kinesin binding / regulation of JNK cascade / regulation of macroautophagy / mitogen-activated protein kinase / negative regulation of intrinsic apoptotic signaling pathway / stress-activated MAPK cascade / axonal growth cone / response to mechanical stimulus / response to UV / JNK cascade / vesicle-mediated transport / cellular response to cadmium ion / cellular response to amino acid starvation / positive regulation of protein metabolic process / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of protein binding / mitochondrial membrane / FCERI mediated MAPK activation / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / regulation of circadian rhythm / cellular response to reactive oxygen species / cellular response to mechanical stimulus / histone deacetylase binding / rhythmic process / regulation of protein localization / cellular senescence / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to oxidative stress / peptidyl-serine phosphorylation / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / cellular response to lipopolysaccharide / neuron projection / positive regulation of apoptotic process / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / synapse / endoplasmic reticulum membrane / positive regulation of gene expression / regulation of DNA-templated transcription / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / signal transduction / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
JIP1, SH3 domain / : / Mitogen-activated protein (MAP) kinase, JNK / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. ...JIP1, SH3 domain / : / Mitogen-activated protein (MAP) kinase, JNK / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 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 8 / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWu, Y. / Mittl, P.R. / Honegger, A. / Batyuk, A. / Plueckthun, A.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_166676 Switzerland
European Research CouncilNEXTBINDERS
CitationJournal: To be published
Title: Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_10_47 in complex JNK1a1 and JIP1 peptide
Authors: Wu, Y. / Mittl, P.R. / Honegger, A. / Batyuk, A. / Plueckthun, A.
History
DepositionDec 1, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionDec 13, 2017ID: 5LEN
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: DD_D12_10_47
B: Mitogen-activated protein kinase 8
C: C-Jun-amino-terminal kinase-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)79,6133
Polymers79,6133
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-16 kcal/mol
Surface area30460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.995, 76.995, 330.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DD_D12_10_47


Mass: 35112.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue
#2: Protein Mitogen-activated protein kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase ...MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1


Mass: 43154.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue
References: UniProt: P45983, mitogen-activated protein kinase
#3: Protein/peptide C-Jun-amino-terminal kinase-interacting protein 1 / JNK-interacting protein 1 / Islet-brain-1 / IB-1 / JNK MAP kinase scaffold protein 1 / Mitogen- ...JNK-interacting protein 1 / Islet-brain-1 / IB-1 / JNK MAP kinase scaffold protein 1 / Mitogen-activated protein kinase 8-interacting protein 1


Mass: 1345.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9WVI9

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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: 3.55 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: PEG 10000 3% w/v Hepes 0.1 M, pH 6.8 Additives (0.033% w/v) 1,5-Naphthalene- disulfonic acid disodium salt 2,5-Pyridinedicarboxylic acid 3,5-Dinitrosalicylic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→46.959 Å / Num. obs: 30294 / % possible obs: 99.9 % / Redundancy: 41.1 % / CC1/2: 1 / Rrim(I) all: 0.14 / Net I/σ(I): 22.99
Reflection shellResolution: 2.7→2.77 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2261 / CC1/2: 0.635 / Rrim(I) all: 7.681 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.959 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 1528 5.06 %
Rwork0.2005 --
obs0.2018 30221 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→46.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 0 0 5283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025385
X-RAY DIFFRACTIONf_angle_d0.4637298
X-RAY DIFFRACTIONf_dihedral_angle_d11.9733252
X-RAY DIFFRACTIONf_chiral_restr0.037831
X-RAY DIFFRACTIONf_plane_restr0.002940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.78720.41161420.37472607X-RAY DIFFRACTION99
2.7872-2.88680.40861250.35252599X-RAY DIFFRACTION100
2.8868-3.00240.34961230.34392624X-RAY DIFFRACTION99
3.0024-3.1390.38981500.29762579X-RAY DIFFRACTION99
3.139-3.30440.26721330.25872601X-RAY DIFFRACTION99
3.3044-3.51140.31921600.24362635X-RAY DIFFRACTION100
3.5114-3.78240.2591280.23042569X-RAY DIFFRACTION100
3.7824-4.16290.24341450.19682620X-RAY DIFFRACTION100
4.1629-4.76470.20561360.1752629X-RAY DIFFRACTION100
4.7647-6.00110.21141290.19172622X-RAY DIFFRACTION100
6.0011-46.96650.17281570.16022608X-RAY DIFFRACTION100
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)
13.29561.0924-1.08472.5084-0.80695.4356-0.2432-0.5249-0.15320.10410.12420.46730.0421-0.90250.06440.880.3135-0.06461.69650.08091.262390.824954.827566.1711
23.51760.5532.56152.78251.37586.9245-0.39931.4144-0.0976-0.24290.4756-0.04350.16230.2082-0.06520.7129-0.16090.00171.89930.02441.122192.62453.894927.386
31.4789-0.30312.06932.29370.70345.2998-0.13130.66420.3635-0.8010.13810.0517-0.76281.0748-0.04390.9015-0.4961-0.0431.31940.17451.117156.284765.63479.1709
44.994-1.17440.92441.3733-0.88613.0546-0.3383-0.28890.28540.16550.2024-0.1538-0.26910.41630.13090.8486-0.3802-0.02211.1844-0.00210.950565.254565.3333.7727
59.4131-2.4928-3.96483.68222.55036.6848-0.44191.0992-0.7465-0.766-0.1353-0.31771.30750.25950.33151.1652-0.2663-0.06621.4724-0.09151.374262.205147.21643.8551
61.3973-1.9193-1.21969.6878-6.2579.98170.30180.18730.7039-0.03930.11080.8142-0.79910.8124-0.42711.0936-0.0627-0.20391.4169-0.04771.459646.401378.659724.6974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 325 )
3X-RAY DIFFRACTION3chain 'B' and (resid 7 through 164 )
4X-RAY DIFFRACTION4chain 'B' and (resid 165 through 335 )
5X-RAY DIFFRACTION5chain 'B' and (resid 336 through 362 )
6X-RAY DIFFRACTION6chain 'C' and (resid 154 through 163 )

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