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- PDB-5uv8: Interleukin-3 Receptor Complex -

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Basic information

Entry
Database: PDB / ID: 5uv8
TitleInterleukin-3 Receptor Complex
Components
  • Interleukin-3 receptor subunit alpha
  • Interleukin-3Interleukin 3
KeywordsSIGNALING PROTEIN / Receptor
Function / homology
Function and homology information


interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / interleukin-3-mediated signaling pathway / cytokine receptor activity / embryonic hemopoiesis / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / positive regulation of tyrosine phosphorylation of STAT protein ...interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / interleukin-3-mediated signaling pathway / cytokine receptor activity / embryonic hemopoiesis / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / nervous system development / RAF/MAP kinase cascade / receptor complex / immune response / external side of plasma membrane / positive regulation of cell population proliferation / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3850 / Interleukin-3 / Interleukin-3 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Growth Hormone; Chain: A; - #10 ...Immunoglobulin-like - #3850 / Interleukin-3 / Interleukin-3 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-3 / Interleukin-3 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBroughton, S.E. / Parker, M.W.
CitationJournal: Nat Commun / Year: 2018
Title: A dual role for the N-terminal domain of the IL-3 receptor in cell signalling.
Authors: Broughton, S.E. / Hercus, T.R. / Nero, T.L. / Kan, W.L. / Barry, E.F. / Dottore, M. / Cheung Tung Shing, K.S. / Morton, C.J. / Dhagat, U. / Hardy, M.P. / Wilson, N.J. / Downton, M.T. / ...Authors: Broughton, S.E. / Hercus, T.R. / Nero, T.L. / Kan, W.L. / Barry, E.F. / Dottore, M. / Cheung Tung Shing, K.S. / Morton, C.J. / Dhagat, U. / Hardy, M.P. / Wilson, N.J. / Downton, M.T. / Schieber, C. / Hughes, T.P. / Lopez, A.F. / Parker, M.W.
History
DepositionFeb 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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 / _atom_site_anisotrop.id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-3 receptor subunit alpha
B: Interleukin-3
G: Interleukin-3 receptor subunit alpha
I: Interleukin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,32513
Polymers94,3334
Non-polymers2,9929
Water1,802100
1
A: Interleukin-3 receptor subunit alpha
B: Interleukin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7075
Polymers47,1662
Non-polymers1,5403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint14 kcal/mol
Surface area20570 Å2
MethodPISA
2
G: Interleukin-3 receptor subunit alpha
I: Interleukin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6188
Polymers47,1662
Non-polymers1,4516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint8 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.039, 132.039, 210.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21G
12B
22I

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRCYSCYSAA28 - 2939 - 274
21THRTHRCYSCYSGC28 - 2939 - 274
12ASNASNASNASNBB15 - 1204 - 109
22ASNASNASNASNID15 - 1204 - 109

NCS ensembles :
ID
2
1

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Components

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Protein , 2 types, 4 molecules AGBI

#1: Protein Interleukin-3 receptor subunit alpha / / IL-3RA


Mass: 33253.570 Da / Num. of mol.: 2 / Fragment: UNP residues 20-307 / Mutation: N212Q, A298V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL3RA, IL3R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P26951
#2: Protein Interleukin-3 / Interleukin 3 / IL-3 / Hematopoietic growth factor / Mast cell growth factor / MCGF / Multipotential colony- ...IL-3 / Hematopoietic growth factor / Mast cell growth factor / MCGF / Multipotential colony-stimulating factor / P-cell-stimulating factor


Mass: 13912.903 Da / Num. of mol.: 2 / Fragment: UNP residues 31-152 / Mutation: W32Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL3 / Production host: Escherichia coli (E. coli) / References: UniProt: P08700

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Sugars , 4 types, 6 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 103 molecules

#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 8000, 200 mM NaCI, 100 mM citrate-phosphate buffer pH 5
PH range: 4.6-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2015
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.7→114.35 Å / Num. obs: 30501 / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 25.7
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.74 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZJ, 1JLI

4jzj

1jli


Resolution: 2.7→114.35 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.849 / SU B: 15.381 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 0.844 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28564 1535 5 %RANDOM
Rwork0.24177 ---
obs0.24404 28930 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.007 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å2-0.82 Å20 Å2
2---1.64 Å20 Å2
3---5.33 Å2
Refinement stepCycle: 1 / Resolution: 2.7→114.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5964 0 197 100 6261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196325
X-RAY DIFFRACTIONr_bond_other_d0.0040.025891
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9738588
X-RAY DIFFRACTIONr_angle_other_deg1.198313552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7423.734308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.387151034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7661550
X-RAY DIFFRACTIONr_chiral_restr0.0740.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216965
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021511
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_it1.5494.2722936
X-RAY DIFFRACTIONr_mcbond_other1.5494.2722935
X-RAY DIFFRACTIONr_mcangle_it2.7636.3813649
X-RAY DIFFRACTIONr_mcangle_other2.7626.3823650
X-RAY DIFFRACTIONr_scbond_it1.4554.6173389
X-RAY DIFFRACTIONr_scbond_other1.4554.6173390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.566.8774940
X-RAY DIFFRACTIONr_long_range_B_refined4.67633.0386518
X-RAY DIFFRACTIONr_long_range_B_other4.67633.046519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A260540.16
12G260540.16
21B124440.12
22I124440.12
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 123 -
Rwork0.315 2053 -
obs--99.95 %

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