[English] 日本語
Yorodumi
- PDB-7nyo: Mutant A541L of SH3 domain of JNK-interacting Protein 1 (JIP1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nyo
TitleMutant A541L of SH3 domain of JNK-interacting Protein 1 (JIP1)
ComponentsSH3 domain of JNK-interacting Protein 1 (JIP1)
KeywordsSIGNALING PROTEIN / SH3 domain of JNK-interacting protein 1 (JIP1)
Function / homology
Function and homology information


dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / JUN kinase binding / protein kinase inhibitor activity / kinesin binding / regulation of JNK cascade / negative regulation of intrinsic apoptotic signaling pathway / vesicle-mediated transport ...dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / JUN kinase binding / protein kinase inhibitor activity / kinesin binding / regulation of JNK cascade / negative regulation of intrinsic apoptotic signaling pathway / vesicle-mediated transport / JNK cascade / mitochondrial membrane / positive regulation of JNK cascade / neuronal cell body / synapse / dendrite / regulation of DNA-templated transcription / endoplasmic reticulum membrane / perinuclear region of cytoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
JIP1, SH3 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...JIP1, SH3 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPerez, L.M. / Ielasi, F.S. / Palencia, A. / Jensen, M.R.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)RC18114CC France
Agence Nationale de la Recherche (ANR)MAPKAssembly France
CitationJournal: Nature / Year: 2022
Title: Visualizing protein breathing motions associated with aromatic ring flipping.
Authors: Marino Perez, L. / Ielasi, F.S. / Bessa, L.M. / Maurin, D. / Kragelj, J. / Blackledge, M. / Salvi, N. / Bouvignies, G. / Palencia, A. / Jensen, M.R.
History
DepositionMar 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: SH3 domain of JNK-interacting Protein 1 (JIP1)
BBB: SH3 domain of JNK-interacting Protein 1 (JIP1)
CCC: SH3 domain of JNK-interacting Protein 1 (JIP1)
DDD: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0159
Polymers30,2744
Non-polymers7415
Water9,458525
1
AAA: SH3 domain of JNK-interacting Protein 1 (JIP1)
BBB: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6215
Polymers15,1372
Non-polymers4853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-20 kcal/mol
Surface area7410 Å2
MethodPISA
2
CCC: SH3 domain of JNK-interacting Protein 1 (JIP1)
DDD: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3934
Polymers15,1372
Non-polymers2562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-5 kcal/mol
Surface area7060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.093, 67.104, 59.142
Angle α, β, γ (deg.)90.000, 126.701, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11DDD-601-

EDO

21BBB-941-

HOH

31CCC-725-

HOH

41DDD-819-

HOH

-
Components

#1: Protein
SH3 domain of JNK-interacting Protein 1 (JIP1) / JIP-1 / JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / ...JIP-1 / JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / Mitogen-activated protein kinase 8-interacting protein 1 / C-Jun-amino-terminal kinase-interacting protein 1


Mass: 7568.447 Da / Num. of mol.: 4 / Mutation: A541L
Source method: isolated from a genetically manipulated source
Details: GHM belongs to expression vector pET28a / Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8IP1, IB1, JIP1, PRKM8IP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UQF2, phosphoinositide 5-phosphatase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 40.5 % / Description: 3D needles
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1-5 % PEG 400 and 2-2.5 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2020
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.4→47.418 Å / Num. obs: 41884 / % possible obs: 91.9 % / Redundancy: 5.3 % / CC1/2: 0.982 / Net I/σ(I): 5.5
Reflection shellResolution: 1.4→1.51 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2095 / CC1/2: 0.74

-
Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NYK

7nyk


Resolution: 1.4→47.418 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.389 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2759 2116 5.071 %
Rwork0.1923 39612 -
all0.197 --
obs-41728 70.412 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.522 Å2
Baniso -1Baniso -2Baniso -3
1-1.592 Å20 Å20.556 Å2
2---0.402 Å20 Å2
3----0.956 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 48 525 2586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132171
X-RAY DIFFRACTIONr_bond_other_d0.0050.0171920
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.662948
X-RAY DIFFRACTIONr_angle_other_deg1.3151.5694434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.55247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.67821.688154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03515334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3661521
X-RAY DIFFRACTIONr_chiral_restr0.0840.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022443
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02516
X-RAY DIFFRACTIONr_nbd_refined0.2780.2514
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.21939
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2927
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2983
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2660.2340
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1350.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.227
X-RAY DIFFRACTIONr_nbd_other0.2280.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2510.222
X-RAY DIFFRACTIONr_mcbond_it3.2311.982967
X-RAY DIFFRACTIONr_mcbond_other3.231.979966
X-RAY DIFFRACTIONr_mcangle_it3.9072.9571209
X-RAY DIFFRACTIONr_mcangle_other3.9052.9611210
X-RAY DIFFRACTIONr_scbond_it3.8862.4021204
X-RAY DIFFRACTIONr_scbond_other3.8842.4021205
X-RAY DIFFRACTIONr_scangle_it4.7873.4691735
X-RAY DIFFRACTIONr_scangle_other4.7853.4691736
X-RAY DIFFRACTIONr_lrange_it7.57628.9232679
X-RAY DIFFRACTIONr_lrange_other6.80526.6252501
X-RAY DIFFRACTIONr_rigid_bond_restr3.21234091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.08820.32388X-RAY DIFFRACTION20.69
1.436-1.4760.347360.281643X-RAY DIFFRACTION16.0104
1.476-1.5180.329930.2541533X-RAY DIFFRACTION39.0302
1.518-1.5650.2631190.2021995X-RAY DIFFRACTION52.7708
1.565-1.6160.2611130.1652250X-RAY DIFFRACTION60.6831
1.616-1.6730.2781220.162468X-RAY DIFFRACTION68.7915
1.673-1.7360.2321500.1522561X-RAY DIFFRACTION74.7038
1.736-1.8070.2691640.1662668X-RAY DIFFRACTION80.5003
1.807-1.8870.3071310.2222787X-RAY DIFFRACTION86.639
1.887-1.9790.4981440.3252865X-RAY DIFFRACTION93.5053
1.979-2.0860.2651450.2172895X-RAY DIFFRACTION99.2815
2.086-2.2120.2811460.2132672X-RAY DIFFRACTION97.61
2.212-2.3650.3871290.2552490X-RAY DIFFRACTION96.2514
2.365-2.5540.2451180.1562413X-RAY DIFFRACTION99.216
2.554-2.7970.2491160.1772224X-RAY DIFFRACTION99.5745
2.797-3.1260.268920.1742002X-RAY DIFFRACTION99.1477
3.126-3.6070.2771010.1571741X-RAY DIFFRACTION98.6609
3.607-4.4120.231940.151479X-RAY DIFFRACTION98.8686
4.412-6.2160.177630.1621177X-RAY DIFFRACTION99.5185

+
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://pdbjlvh1.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