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- PDB-3di3: Crystal structure of the complex of human interleukin-7 with glyc... -

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Basic information

Entry
Database: PDB / ID: 3di3
TitleCrystal structure of the complex of human interleukin-7 with glycosylated human interleukin-7 receptor alpha ectodomain
Components
  • Interleukin-7
  • Interleukin-7 receptor subunit alpha
KeywordsCYTOKINE/CYTOKINE RECEPTOR / interleukin / cytokine / cytokine receptor / ectodomain / Glycoprotein / Growth factor / Secreted / Disease mutation / Membrane / Phosphoprotein / Receptor / SCID / Transmembrane / CYTOKINE-CYTOKINE RECEPTOR COMPLEX
Function / homology
Function and homology information


interleukin-7 receptor binding / interleukin-7 receptor activity / negative regulation of T cell mediated cytotoxicity / regulation of DNA recombination / positive regulation of T cell differentiation in thymus / positive regulation of cytokine-mediated signaling pathway / positive regulation of receptor signaling pathway via STAT / interleukin-7-mediated signaling pathway / negative regulation of T cell apoptotic process / cellular homeostasis ...interleukin-7 receptor binding / interleukin-7 receptor activity / negative regulation of T cell mediated cytotoxicity / regulation of DNA recombination / positive regulation of T cell differentiation in thymus / positive regulation of cytokine-mediated signaling pathway / positive regulation of receptor signaling pathway via STAT / interleukin-7-mediated signaling pathway / negative regulation of T cell apoptotic process / cellular homeostasis / cytokine receptor activity / positive regulation of T cell differentiation / regulation of cell size / B cell homeostasis / T cell homeostasis / humoral immune response / B cell proliferation / hemopoiesis / lymph node development / bone resorption / antigen binding / positive regulation of chemokine production / positive regulation of B cell proliferation / Interleukin-7 signaling / cytokine activity / animal organ morphogenesis / T cell mediated cytotoxicity / growth factor activity / positive regulation of receptor signaling pathway via JAK-STAT / clathrin-coated endocytic vesicle membrane / cell morphogenesis / cytokine-mediated signaling pathway / T cell differentiation in thymus / cell-cell signaling / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / extracellular matrix / gene expression / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / : / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Growth Hormone; Chain: A; - #50 / Interleukin-7 / Interleukin-7 superfamily / Interleukin 7 / Interleukin-7 and interleukin-9 family. / Interleukin-7/Interleukin-9, conserved site / Interleukin-7 and -9 signature. / Immunoglobulin-like - #1870 / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain ...Growth Hormone; Chain: A; - #50 / Interleukin-7 / Interleukin-7 superfamily / Interleukin 7 / Interleukin-7 and interleukin-9 family. / Interleukin-7/Interleukin-9, conserved site / Interleukin-7 and -9 signature. / Immunoglobulin-like - #1870 / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Growth Hormone; Chain: A; / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-7 / Interleukin-7 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMcElroy, C.A. / Dohm, J.A. / Walsh, S.T.R.
CitationJournal: Structure / Year: 2009
Title: Structural and Biophysical Studies of the Human IL-7/IL-7Ralpha Complex.
Authors: McElroy, C.A. / Dohm, J.A. / Walsh, S.T.
History
DepositionJun 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Interleukin-7
B: Interleukin-7 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5105
Polymers43,2362
Non-polymers1,2733
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint5 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.573, 68.235, 112.273
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 Interleukin-7 / IL-7


Mass: 17545.453 Da / Num. of mol.: 1 / Fragment: UNP residues 26 to 177 / Mutation: E106A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL7 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RP / References: UniProt: P13232
#2: Protein Interleukin-7 receptor subunit alpha / IL-7R-alpha / CD127 antigen / CDw127


Mass: 25691.020 Da / Num. of mol.: 1
Fragment: UNP residues 21 to 239 (ligand binding ectodomain)
Mutation: I118V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL7R / Plasmid: pMT-BipA / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider S2 insect cells / References: UniProt: P16871
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 292 K / pH: 7.4
Details: 18% w/v PEG 3350, 0.1 M HEPES pH 7.4, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 19-ID10.97888
SYNCHROTRONAPS 19-ID20.97932
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 20, 2006
ADSC QUANTUM 3152CCDSep 5, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978881
20.979321
ReflectionResolution: 2.9→30 Å / Num. obs: 8746 / % possible obs: 91.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 1.7 / % possible all: 48.1

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→15 Å / Occupancy max: 1 / Occupancy min: 1
Isotropic thermal model: PDB ENTRY 3DI2 and a platinum derivative
σ(F): 2
RfactorNum. reflection% reflection
Rfree0.267 447 4.5 %
Rwork0.229 --
obs0.229 8746 88.7 %
all-9857 -
Solvent computationBsol: 58.89 Å2
Displacement parametersBiso mean: 83.16 Å2
Baniso -1Baniso -2Baniso -3
1-10.274 Å20 Å20 Å2
2--9.935 Å20 Å2
3----20.209 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 83 15 2500
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5351.5
X-RAY DIFFRACTIONc_mcangle_it2.7592
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it3.1742.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION6

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