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- PDB-3up1: Crystal structure of the unliganded human interleukin-7 receptor ... -

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Basic information

Entry
Database: PDB / ID: 3up1
TitleCrystal structure of the unliganded human interleukin-7 receptor extracellular domain
ComponentsInterleukin-7 receptor subunit alpha
KeywordsIMMUNE SYSTEM / cytokine receptor / fibronectin type 3 fold / membrane and soluble / glycosylation
Function / homology
Function and homology information


interleukin-7 receptor activity / positive regulation of receptor signaling pathway via STAT / negative regulation of T cell mediated cytotoxicity / regulation of DNA recombination / positive regulation of T cell differentiation in thymus / negative regulation of T cell apoptotic process / cytokine receptor activity / regulation of cell size / B cell proliferation / T cell homeostasis ...interleukin-7 receptor activity / positive regulation of receptor signaling pathway via STAT / negative regulation of T cell mediated cytotoxicity / regulation of DNA recombination / positive regulation of T cell differentiation in thymus / negative regulation of T cell apoptotic process / cytokine receptor activity / regulation of cell size / B cell proliferation / T cell homeostasis / B cell homeostasis / hemopoiesis / lymph node development / Interleukin-7 signaling / antigen binding / positive regulation of receptor signaling pathway via JAK-STAT / clathrin-coated endocytic vesicle membrane / cell morphogenesis / T cell mediated cytotoxicity / cytokine-mediated signaling pathway / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / gene expression / T cell differentiation in thymus / 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 / signal transduction / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
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 / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins ...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 / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / 2-acetamido-2-deoxy-beta-D-galactopyranose / Interleukin-7 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMcElroy, C.A. / Holland, P.J. / Walsh, S.T.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural reorganization of the interleukin-7 signaling complex.
Authors: McElroy, C.A. / Holland, P.J. / Zhao, P. / Lim, J.M. / Wells, L. / Eisenstein, E. / Walsh, S.T.
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
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 / 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_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _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_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-7 receptor subunit alpha
B: Interleukin-7 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,62916
Polymers51,3822
Non-polymers2,24714
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-58 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.424, 101.259, 151.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1056-

HOH

21A-1057-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Interleukin-7 receptor subunit alpha / IL-7 receptor subunit alpha / IL-7R subunit alpha / IL-7R-alpha / IL-7RA / CDw127


Mass: 25691.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL7R / Plasmid: pMT-BipA / Production host: Drosophila (fruit flies) / Strain (production host): Schneider S2 insect cells / References: UniProt: P16871

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Sugars , 3 types, 5 molecules

#2: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 144 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 292 K / pH: 8.5
Details: 1.26M (NH4)2SO4, 0.1 M Tris-HCl pH 8.5, 0.2 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03337
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03337 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 34331 / % possible obs: 99.4 % / Redundancy: 6.7 %

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→14.93 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.79 / σ(F): 1.34 / Phase error: 28.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 2634 7.7 %
Rwork0.214 --
obs0.217 34199 99.3 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.51 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3114 Å2-0 Å2-0 Å2
2---2.8108 Å20 Å2
3----0.5006 Å2
Refinement stepCycle: LAST / Resolution: 2.15→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 139 135 3501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083460
X-RAY DIFFRACTIONf_angle_d1.244677
X-RAY DIFFRACTIONf_dihedral_angle_d16.0781284
X-RAY DIFFRACTIONf_chiral_restr0.086531
X-RAY DIFFRACTIONf_plane_restr0.004569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.1890.60451260.59721574X-RAY DIFFRACTION95
2.189-2.2310.47021260.50641623X-RAY DIFFRACTION97
2.231-2.27640.49961220.43781612X-RAY DIFFRACTION97
2.2764-2.32570.48381360.3911650X-RAY DIFFRACTION99
2.3257-2.37960.47281430.34221612X-RAY DIFFRACTION99
2.3796-2.43880.34691400.27371650X-RAY DIFFRACTION100
2.4388-2.50450.32531420.24441659X-RAY DIFFRACTION100
2.5045-2.57780.35251470.22931630X-RAY DIFFRACTION100
2.5778-2.66060.26591250.22641680X-RAY DIFFRACTION100
2.6606-2.75510.23971280.24121670X-RAY DIFFRACTION100
2.7551-2.86460.28441430.23821665X-RAY DIFFRACTION100
2.8646-2.9940.31611440.22971664X-RAY DIFFRACTION100
2.994-3.15050.28011560.23641649X-RAY DIFFRACTION100
3.1505-3.34580.29811370.22351683X-RAY DIFFRACTION100
3.3458-3.60080.23981400.20271676X-RAY DIFFRACTION100
3.6008-3.9570.20621290.17011698X-RAY DIFFRACTION100
3.957-4.51560.17291480.14761683X-RAY DIFFRACTION100
4.5156-5.63780.17951550.14281721X-RAY DIFFRACTION100
5.6378-14.92690.22161470.19371766X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4211-0.3850.44852.68271.55052.5128-0.1317-0.187-0.033-0.0075-0.13060.27390.0257-0.22410.21830.2831-0.055-0.03070.169-0.0450.22644.549615.931851.0651
22.31090.98120.65483.46780.47551.31940.0154-0.14560.05690.0263-0.00580.1815-0.23990.0313-0.00410.2555-0.05560.00840.1763-0.0380.141554.8337.166372.5353
33.87882.66330.70662.74721.23032.73880.3877-0.32970.22050.5648-0.35340.1760.0855-0.1107-0.02110.3683-0.00310.05060.21970.00190.258162.1843.854333.4318
40.6396-0.0237-0.65133.91272.30994.49310.14440.09930.0168-0.01910.0091-0.15840.0368-0.3547-0.16730.1926-0.0634-0.00140.30980.050.200351.557920.438114.5609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 12:107)
2X-RAY DIFFRACTION2(chain A and resid 108:212)
3X-RAY DIFFRACTION3(chain B and resid 16:102)
4X-RAY DIFFRACTION4(chain B and resid 103:211)

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