[English] 日本語
Yorodumi
- PDB-2fpf: Crystal structure of the ib1 sh3 dimer at low resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fpf
TitleCrystal structure of the ib1 sh3 dimer at low resolution
ComponentsC-jun-amino-terminal kinase interacting protein 1
KeywordsSIGNALING PROTEIN / SCAFFOLD PROTEIN 1 / ISLET-BRAIN-1 / IB-1 / MITOGEN-ACTIVATED PROTEIN KINASE 8-INTERACTING PROTEIN 1 / JIP-1 RELATED PROTEIN / JRP
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 / negative regulation of JNK cascade / JUN kinase binding / mitogen-activated protein kinase kinase kinase binding / mitogen-activated protein kinase kinase binding / dendritic growth cone / kinesin binding ...dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / negative regulation of JNK cascade / JUN kinase binding / mitogen-activated protein kinase kinase kinase binding / mitogen-activated protein kinase kinase binding / dendritic growth cone / kinesin binding / regulation of JNK cascade / negative regulation of intrinsic apoptotic signaling pathway / axonal growth cone / JNK cascade / vesicle-mediated transport / mitochondrial membrane / positive regulation of JNK cascade / neuron projection / axon / neuronal cell body / dendrite / synapse / endoplasmic reticulum membrane / regulation of DNA-templated transcription / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / signal transduction / membrane / identical protein binding / nucleus / cytosol / cytoplasm
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 / SH3 Domains / SH3 type barrels. / Src homology 3 domains ...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 / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKristensen, O. / Dar, I. / Gajhede, M.
Citation
#1: Journal: Science / Year: 1997
Title: A cytoplasmic inhibitor of the JNK signal transduction pathway
Authors: Dickens, M. / Rogers, J.S. / Cavanagh, J. / Raitano, A. / Xia, Z. / Halpern, J.R. / Greenberg, M.E. / Sawyers, C.L. / Davis, R.J.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: IB1, a JIP-1-related nuclear protein present in insulin-secreting cells
Authors: Bonny, C. / Nicod, P. / Waeber, G.
#3: Journal: J.Biol.Chem. / Year: 2003
Title: Recruitment of JNK to JIP1 and JNK-dependent JIP1 phosphorylation regulates JNK module dynamics and activation
Authors: Nihalani, D. / Wong, H.N. / Holzman, L.B.
#4: Journal: Mol.Cell.Biol. / Year: 1999
Title: The JIP group of mitogen-activated protein kinase scaffold proteins
Authors: Yasuda, J. / Whitmarsh, A.J. / Cavanagh, J. / Sharma, M. / Davis, R.J.
History
DepositionJan 16, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-jun-amino-terminal kinase interacting protein 1
B: C-jun-amino-terminal kinase interacting protein 1
C: C-jun-amino-terminal kinase interacting protein 1
D: C-jun-amino-terminal kinase interacting protein 1


Theoretical massNumber of molelcules
Total (without water)33,8534
Polymers33,8534
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.868, 57.000, 145.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.45925, -0.42769, 0.77857), (-0.43943, -0.87109, -0.21931), (0.772, -0.24141, -0.58799)-134.52009, 5.49, 256.50337
3given(-0.57065, 0.81133, 0.12688), (0.53193, 0.48291, -0.69559), (-0.62563, -0.32945, -0.70714)8.70527, 107.03895, 284.67057
4given(-0.4872, -0.5057, -0.71197), (-0.51472, -0.49233, 0.70191), (-0.70548, 0.70844, -0.02043)124.15242, -137.62102, 189.48617

-
Components

#1: Protein
C-jun-amino-terminal kinase interacting protein 1 / JNK-interacting protein 1 / JIP-1 / JNK MAP kinase scaffold protein 1 / Islet-brain-1 / IB-1 / ...JNK-interacting protein 1 / JIP-1 / JNK MAP kinase scaffold protein 1 / Islet-brain-1 / IB-1 / Mitogen-activated protein kinase 8-interacting protein 1 / JIP-1-related protein / JRP


Mass: 8463.264 Da / Num. of mol.: 4 / Fragment: SH3 DOMAIN, RESIDUES -1-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mapk8ip1, Ib1, Jip1 / Plasmid: PGEX 4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA BL21(DE3)PLYSS / References: UniProt: Q9R237

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: SODIUM CITRATE, HEPES, HYDROGEN PEROXIDE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 8075 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 12.07
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.461 / % possible all: 100

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FPD

2fpd


Resolution: 3→28.77 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 230208.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 572 7.4 %RANDOM
Rwork0.224 ---
obs0.224 7679 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.58 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1--5.51 Å20 Å20 Å2
2--8.73 Å20 Å2
3----3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 0 0 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.691.5
X-RAY DIFFRACTIONc_mcangle_it10.392
X-RAY DIFFRACTIONc_scbond_it14.422
X-RAY DIFFRACTIONc_scangle_it20.592.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 88 7.4 %
Rwork0.288 1094 -
obs--89 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

+
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