[English] 日本語
Yorodumi
- PDB-6f5e: Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_1... -

+
Open data


ID or keywords:

Loading...

-
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


dentate gyrus mossy fiber / positive regulation of cell killing / regulation of CD8-positive, alpha-beta T cell proliferation / JUN phosphorylation / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / basal dendrite / negative regulation of JUN kinase activity / JUN kinase activity / Activation of BIM and translocation to mitochondria ...dentate gyrus mossy fiber / positive regulation of cell killing / regulation of CD8-positive, alpha-beta T cell proliferation / JUN phosphorylation / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / basal dendrite / negative regulation of JUN kinase activity / JUN kinase activity / Activation of BIM and translocation to mitochondria / WNT5:FZD7-mediated leishmania damping / MAP kinase scaffold activity / JUN kinase binding / negative regulation of JNK cascade / histone deacetylase regulator activity / mitogen-activated protein kinase kinase kinase binding / regulation of JNK cascade / positive regulation of cyclase activity / mitogen-activated protein kinase kinase binding / positive regulation of protein localization to mitochondrion / NRAGE signals death through JNK / negative regulation of intrinsic apoptotic signaling pathway / Activation of the AP-1 family of transcription factors / peptidyl-threonine phosphorylation / dendritic growth cone / Fc-epsilon receptor signaling pathway / energy homeostasis / response to UV / positive regulation of protein metabolic process / mitogen-activated protein kinase / positive regulation of NLRP3 inflammasome complex assembly / stress-activated MAPK cascade / JNK cascade / negative regulation of protein binding / response to mechanical stimulus / axonal growth cone / kinesin binding / vesicle-mediated transport / regulation of macroautophagy / cellular response to amino acid starvation / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / protein serine/threonine kinase binding / FCERI mediated MAPK activation / cellular response to reactive oxygen species / peptidyl-serine phosphorylation / positive regulation of JNK cascade / cellular senescence / regulation of circadian rhythm / cellular response to mechanical stimulus / histone deacetylase binding / mitochondrial membrane / MAPK cascade / Signaling by ALK fusions and activated point mutants / regulation of protein localization / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to lipopolysaccharide / cellular response to oxidative stress / response to oxidative stress / cell body / protein phosphatase binding / Oxidative Stress Induced Senescence / protein phosphorylation / neuron projection / positive regulation of apoptotic process / protein serine kinase activity / axon / protein serine/threonine kinase activity / positive regulation of gene expression / negative regulation of apoptotic process / regulation of DNA-templated transcription / dendrite / protein kinase binding / synapse / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / enzyme binding / 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 / 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more