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- PDB-4ydy: CRYSTAL STRUCTURE OF DARPIN 44C12V5 IN COMPLEX WITH HUMAN IL-4 -

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Basic information

Entry
Database: PDB / ID: 4ydy
TitleCRYSTAL STRUCTURE OF DARPIN 44C12V5 IN COMPLEX WITH HUMAN IL-4
Components
  • DARPIN 44C12V5
  • Interleukin-4
KeywordsCYTOKINE/DE NOVO PROTEIN / ALTERNATIVE SCAFFOLD / CYTOKINE-DE NOVO PROTEIN complex
Function / homology
Function and homology information


interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / positive regulation of cellular respiration / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / regulation of isotype switching / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation ...interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / positive regulation of cellular respiration / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / regulation of isotype switching / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation / interleukin-4-mediated signaling pathway / neuroinflammatory response / positive regulation of isotype switching to IgG isotypes / positive regulation of interleukin-13 production / macrophage activation / positive regulation of amyloid-beta clearance / myeloid dendritic cell differentiation / positive regulation of MHC class II biosynthetic process / type 2 immune response / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / negative regulation of osteoclast differentiation / positive regulation of ATP biosynthetic process / positive regulation of macroautophagy / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / regulation of immune response / negative regulation of endothelial cell apoptotic process / cell surface receptor signaling pathway via JAK-STAT / cholesterol metabolic process / positive regulation of B cell proliferation / positive regulation of T cell proliferation / B cell differentiation / cytokine activity / T cell activation / growth factor activity / positive regulation of receptor-mediated endocytosis / negative regulation of inflammatory response / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / immune response / positive regulation of cell migration / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / : / extracellular region
Similarity search - Function
Interleukin-4 / Interleukin 4 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Growth Hormone; Chain: A; - #10 / Ankyrin repeat-containing domain / Four-helical cytokine-like, core / Growth Hormone; Chain: A; ...Interleukin-4 / Interleukin 4 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Growth Hormone; Chain: A; - #10 / Ankyrin repeat-containing domain / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Interleukin-4
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF DARPIN 44C12V5 IN COMPLEX WITH HUMAN IL-4
Authors: Teplyakov, A. / Obmolova, G. / Gilliland, G.
History
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DARPIN 44C12V5
I: Interleukin-4
B: DARPIN 44C12V5
J: Interleukin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2587
Polymers66,0154
Non-polymers2433
Water6,557364
1
A: DARPIN 44C12V5
I: Interleukin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1924
Polymers33,0072
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DARPIN 44C12V5
J: Interleukin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0673
Polymers33,0072
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.250, 113.660, 117.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DARPIN 44C12V5


Mass: 17887.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Interleukin-4 / IL-4 / B-cell stimulatory factor 1 / BSF-1 / Binetrakin / Lymphocyte stimulatory factor 1 / Pitrakinra


Mass: 15120.445 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL4 / Production host: Escherichia coli (E. coli) / References: UniProt: P05112
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 18% PEG 3350, 0.2 M LITHIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.5 0.1 M SODIUM ACETATE, PH 4.5, 18% GLYCEROL
PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 46738 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.9 / % possible all: 86.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B8U (IL-4), 2J8S (Darpin)

2b8u

2j8s


Resolution: 2→27.8 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / SU B: 3.403 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.23943 954 2 %RANDOM
Rwork0.20161 ---
obs0.2024 45618 91.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å20 Å2
2--1.68 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4240 0 16 364 4620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224321
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9821.965856
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5125556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61625.181193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97115730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9991521
X-RAY DIFFRACTIONr_chiral_restr0.0690.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023208
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.83222782
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.65844413
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it35.157881539
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it36.644881443
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 73 -
Rwork0.202 3374 -
obs--86.5 %

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