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- PDB-4pxj: Crystallographic structure of the LZII fragment (anti-parallel or... -

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Basic information

Entry
Database: PDB / ID: 4pxj
TitleCrystallographic structure of the LZII fragment (anti-parallel orientation) from JIP3
ComponentsC-Jun-amino-terminal kinase-interacting protein 3
KeywordsPROTEIN BINDING / Leucine zipper / scaffold protein / axonal transport
Function / homology
Function and homology information


anterograde axonal protein transport / MAP-kinase scaffold activity / JUN kinase binding / axon regeneration / axon development / kinesin binding / regulation of JNK cascade / vesicle-mediated transport / axon cytoplasm / positive regulation of JNK cascade ...anterograde axonal protein transport / MAP-kinase scaffold activity / JUN kinase binding / axon regeneration / axon development / kinesin binding / regulation of JNK cascade / vesicle-mediated transport / axon cytoplasm / positive regulation of JNK cascade / signaling receptor complex adaptor activity / cell body / growth cone / cytoplasmic vesicle / protein stabilization / axon / Golgi membrane / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / cytoplasm
Similarity search - Function
WD40 repeated domain / JNK-interacting protein, leucine zipper II / JNK-interacting protein 3/4 / JNK-interacting protein leucine zipper II / JNK/Rab-associated protein-1, N-terminal / RILP homology 1 domain / RH1 domain / RH2 domain / RH1 domain profile. / RH2 domain profile. ...WD40 repeated domain / JNK-interacting protein, leucine zipper II / JNK-interacting protein 3/4 / JNK-interacting protein leucine zipper II / JNK/Rab-associated protein-1, N-terminal / RILP homology 1 domain / RH1 domain / RH2 domain / RH1 domain profile. / RH2 domain profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
GUANIDINE / C-Jun-amino-terminal kinase-interacting protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsLlinas, P. / Menetrey, J.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Structure of a truncated form of leucine zipper II of JIP3 reveals an unexpected antiparallel coiled-coil arrangement.
Authors: Llinas, P. / Chenon, M. / Nguyen, T.Q. / Moreira, C. / de Regibus, A. / Coquard, A. / Ramos, M.J. / Guerois, R. / Fernandes, P.A. / Menetrey, J.
History
DepositionMar 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-Jun-amino-terminal kinase-interacting protein 3
B: C-Jun-amino-terminal kinase-interacting protein 3
C: C-Jun-amino-terminal kinase-interacting protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,22211
Polymers20,6643
Non-polymers5598
Water3,729207
1
A: C-Jun-amino-terminal kinase-interacting protein 3
B: C-Jun-amino-terminal kinase-interacting protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2389
Polymers13,7762
Non-polymers4627
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-34 kcal/mol
Surface area8090 Å2
MethodPISA
2
C: C-Jun-amino-terminal kinase-interacting protein 3
hetero molecules

C: C-Jun-amino-terminal kinase-interacting protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9684
Polymers13,7762
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area3430 Å2
ΔGint-49 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.826, 63.040, 50.219
Angle α, β, γ (deg.)90.00, 97.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein C-Jun-amino-terminal kinase-interacting protein 3 / JIP-3 / JNK-interacting protein 3 / JNK MAP kinase scaffold protein 3 / Mitogen-activated protein ...JIP-3 / JNK-interacting protein 3 / JNK MAP kinase scaffold protein 3 / Mitogen-activated protein kinase 8-interacting protein 3


Mass: 6887.882 Da / Num. of mol.: 3 / Fragment: Leucine zipper II fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8IP3, JIP3, KIAA1066 / Plasmid: pGST//1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UPT6
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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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: 5.23 Å3/Da / Density % sol: 76.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 1.6 M SAM, 0.1 M citrate pH 5.5, 2 % PEG 400, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9788
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.06→43.136 Å / Num. obs: 26642 / % possible obs: 99.8 % / Observed criterion σ(I): 6.72 / Biso Wilson estimate: 32.57 Å2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→38.67 Å / σ(F): 5.48 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.205 1997 7.5 %
Rwork0.18 --
all-26643 -
obs-26641 99.86 %
Displacement parametersBiso mean: 43.9 Å2
Refinement stepCycle: LAST / Resolution: 2.06→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 34 207 1588
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.62
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr

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