[English] 日本語
Yorodumi
- PDB-2fpd: Sad structure determination: crystal structure of the intrinsic d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fpd
TitleSad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein
ComponentsC-jun-amino-terminal kinase interacting protein 1
KeywordsSIGNALING PROTEIN / SRC-HOMOLOGY 3 (SH3) DOMAIN / ALL BETA STRUCTURE
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 / axonal growth cone / negative regulation of intrinsic apoptotic signaling pathway / vesicle-mediated transport / JNK cascade / mitochondrial membrane / positive regulation of JNK cascade / neuron projection / axon / neuronal cell body / synapse / dendrite / regulation of DNA-templated transcription / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / signal transduction / identical protein binding / membrane / nucleus / 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 / 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
trehalose / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 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 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0987
Polymers29,5644
Non-polymers5343
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-47 kcal/mol
Surface area12440 Å2
MethodPISA
2
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,19714
Polymers59,1288
Non-polymers1,0696
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14220 Å2
ΔGint-105 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.486, 114.486, 48.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
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: 7390.998 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
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: AMMONIUM SULFATE, BICINE, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.967
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 5, 2003
RadiationMonochromator: BENDABLE ASYMMETRICALLY CUT SI(111) CRYSTAL IN COMBINATION WITH VERTICALLY FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 37925 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 8.02 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 7.7
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 8.24 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.28 / Rsym value: 0.34 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
ARP/wARPmodel building
CCP4model building
CNS1.1refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→24.64 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1632143.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: EXPERIMENTAL PHASES WERE USED THROUGHOUT IN THE REFINEMENT, WHICH WAS BASED ON THE MLHL TARGET FUNCTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1947 5.1 %RANDOM
Rwork0.184 ---
obs0.184 37925 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.59 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2--0.82 Å20 Å2
3----1.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.05→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 33 249 2382
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.05→2.16 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.248 303 5.7 %
Rwork0.191 5051 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4TRE_XPLOR_PARAM.TXTTRE_XPLOR_TOP.TXT

+
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