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- PDB-7nyn: Mutant Y526A of SH3 domain of JNK-interacting Protein 1 (JIP1) -

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Basic information

Entry
Database: PDB / ID: 7nyn
TitleMutant Y526A 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 / regulation of JNK cascade / mitogen-activated protein kinase kinase binding / mitogen-activated protein kinase kinase kinase binding / negative regulation of intrinsic apoptotic signaling pathway / dendritic growth cone ...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 / regulation of JNK cascade / mitogen-activated protein kinase kinase binding / mitogen-activated protein kinase kinase kinase binding / negative regulation of intrinsic apoptotic signaling pathway / dendritic growth cone / protein kinase inhibitor activity / kinesin binding / axonal growth cone / vesicle-mediated transport / JNK cascade / positive regulation of JNK cascade / mitochondrial membrane / neuronal cell body / synapse / 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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.537 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)
EEE: SH3 domain of JNK-interacting Protein 1 (JIP1)
FFF: SH3 domain of JNK-interacting Protein 1 (JIP1)
GGG: SH3 domain of JNK-interacting Protein 1 (JIP1)
HHH: SH3 domain of JNK-interacting Protein 1 (JIP1)
III: SH3 domain of JNK-interacting Protein 1 (JIP1)
JJJ: SH3 domain of JNK-interacting Protein 1 (JIP1)
KKK: SH3 domain of JNK-interacting Protein 1 (JIP1)
LLL: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,59743
Polymers89,21112
Non-polymers4,38531
Water12,611700
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)15,9358
Polymers14,8692
Non-polymers1,0666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-13 kcal/mol
Surface area7780 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)16,05010
Polymers14,8692
Non-polymers1,1818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-27 kcal/mol
Surface area7340 Å2
MethodPISA
3
EEE: SH3 domain of JNK-interacting Protein 1 (JIP1)
FFF: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2655
Polymers14,8692
Non-polymers3963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-20 kcal/mol
Surface area6890 Å2
MethodPISA
4
GGG: SH3 domain of JNK-interacting Protein 1 (JIP1)
HHH: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,99410
Polymers14,8692
Non-polymers1,1258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-22 kcal/mol
Surface area7430 Å2
MethodPISA
5
III: SH3 domain of JNK-interacting Protein 1 (JIP1)
JJJ: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2655
Polymers14,8692
Non-polymers3963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-18 kcal/mol
Surface area6550 Å2
MethodPISA
6
KKK: SH3 domain of JNK-interacting Protein 1 (JIP1)
LLL: SH3 domain of JNK-interacting Protein 1 (JIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0895
Polymers14,8692
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-19 kcal/mol
Surface area6540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.639, 62.485, 87.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11AAA-736-

HOH

21AAA-753-

HOH

31BBB-748-

HOH

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Components

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Protein , 1 types, 12 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJKKKLLL

#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: 7434.271 Da / Num. of mol.: 12
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

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Non-polymers , 7 types, 731 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.2 Å3/Da / Density % sol: 61 % / Description: 3D well defined needless
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1-5 % PEG 400, 2-2.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.537→49.35 Å / Num. obs: 329963 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.99 / Net I/σ(I): 11.9
Reflection shellResolution: 1.54→1.63 Å / Num. unique obs: 52785 / CC1/2: 0.31 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC7.1.007refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NYK

7nyk


Resolution: 1.537→49.35 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.872 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1796 1798 1.051 %
Rwork0.1378 169316 -
all0.138 --
obs-171114 99.932 %
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: 37.594 Å2
Baniso -1Baniso -2Baniso -3
1--1.416 Å20 Å20 Å2
2--3.466 Å2-0 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 1.537→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6057 0 280 700 7037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0136526
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175879
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.6588798
X-RAY DIFFRACTIONr_angle_other_deg1.4151.57213505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.955729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.58221.727440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72915960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7751560
X-RAY DIFFRACTIONr_chiral_restr0.0990.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021567
X-RAY DIFFRACTIONr_nbd_refined0.210.21122
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.26081
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22938
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.23404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2501
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.231
X-RAY DIFFRACTIONr_nbd_other0.2260.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.224
X-RAY DIFFRACTIONr_mcbond_it5.3183.3872928
X-RAY DIFFRACTIONr_mcbond_other5.2683.3862927
X-RAY DIFFRACTIONr_mcangle_it5.8945.0493647
X-RAY DIFFRACTIONr_mcangle_other5.8965.0513648
X-RAY DIFFRACTIONr_scbond_it9.234.1713598
X-RAY DIFFRACTIONr_scbond_other9.2294.1713599
X-RAY DIFFRACTIONr_scangle_it10.6725.9755148
X-RAY DIFFRACTIONr_scangle_other10.6715.9755149
X-RAY DIFFRACTIONr_lrange_it8.47540.9677033
X-RAY DIFFRACTIONr_lrange_other8.47440.9727034
X-RAY DIFFRACTIONr_rigid_bond_restr5.518312405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.537-1.5770.3791310.411122970.411125270.5810.66399.20970.403
1.577-1.620.3641280.361120700.361121980.6950.7211000.351
1.62-1.6670.3121250.301117720.301118970.7990.8151000.29
1.667-1.7190.281210.236113870.237115090.8660.87499.99130.216
1.719-1.7750.2241180.192110970.193112160.840.90599.99110.169
1.775-1.8370.2081140.152107340.152108480.9380.9481000.127
1.837-1.9060.2031100.126103740.127104840.9410.9651000.103
1.906-1.9840.1591060.10999930.11100990.970.9731000.089
1.984-2.0720.1741020.11195810.11296830.9670.9731000.095
2.072-2.1730.14970.10291670.10392640.9710.981000.09
2.173-2.290.159930.09687370.09688300.9690.9811000.085
2.29-2.4290.15870.09582860.09683730.9740.981000.086
2.429-2.5960.158830.09978020.09978850.9670.9791000.092
2.596-2.8040.137780.10372850.10473630.9750.9791000.101
2.804-3.070.19710.12967240.1367950.9620.9721000.134
3.07-3.4310.202650.15161150.15161810.960.9799.98380.161
3.431-3.9590.172580.13354450.13455040.9720.97899.98180.152
3.959-4.840.15490.10746370.10746860.9780.9861000.133
4.84-6.8130.172380.15736440.15736820.9720.9721000.189
6.813-49.350.205240.21921690.21921970.9540.95499.81790.28

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