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- PDB-1gh7: CRYSTAL STRUCTURE OF THE COMPLETE EXTRACELLULAR DOMAIN OF THE BET... -

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Basic information

Entry
Database: PDB / ID: 1gh7
TitleCRYSTAL STRUCTURE OF THE COMPLETE EXTRACELLULAR DOMAIN OF THE BETA-COMMON RECEPTOR OF IL-3, IL-5, AND GM-CSF
ComponentsCYTOKINE RECEPTOR COMMON BETA CHAIN
KeywordsCYTOKINE RECEPTOR / Dimer of interlocking chains of fibronectin-III domains Four fibronectin-III domains per chain
Function / homology
Function and homology information


Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway ...Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / cytokine receptor activity / cell surface receptor signaling pathway via JAK-STAT / Interleukin-3, Interleukin-5 and GM-CSF signaling / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / coreceptor activity / cytokine-mediated signaling pathway / signaling receptor activity / RAF/MAP kinase cascade / response to lipopolysaccharide / external side of plasma membrane / signal transduction / plasma membrane
Similarity search - Function
: / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Interferon-alpha/beta receptor, fibronectin type III / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...: / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Interferon-alpha/beta receptor, fibronectin type III / Fibronectin type 3 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
Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsCarr, P.D. / Gustin, S.E. / Church, A.P. / Murphy, J.M. / Ford, S.C. / Mann, D.A. / Woltring, D.M. / Walker, I. / Ollis, D.L. / Young, I.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structure of the complete extracellular domain of the common beta subunit of the human GM-CSF, IL-3, and IL-5 receptors reveals a novel dimer configuration.
Authors: Carr, P.D. / Gustin, S.E. / Church, A.P. / Murphy, J.M. / Ford, S.C. / Mann, D.A. / Woltring, D.M. / Walker, I. / Ollis, D.L. / Young, I.G.
History
DepositionNov 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 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_validate_chiral / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_sheet
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 / _struct_sheet.number_strands
Revision 2.2Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOKINE RECEPTOR COMMON BETA CHAIN
B: CYTOKINE RECEPTOR COMMON BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9396
Polymers95,6252
Non-polymers2,3144
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-19 kcal/mol
Surface area43970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.7, 185.7, 103.3
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number146
Space group name H-MH3

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Components

#1: Protein CYTOKINE RECEPTOR COMMON BETA CHAIN


Mass: 47812.473 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN / Mutation: N328Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell line: CELL LINE HL60 DERIVED FROM A PROMYELOCYTIC LEUKEMIA
Plasmid: PBACPAK8 (CLONTECH)
Cell line (production host): BTI-TN-5BI-4 (HIGH FIVE) INVITROGEN
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32927
#2: 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.: 2
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
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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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: 3.58 Å3/Da / Density % sol: 65.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG MME 5000, Phosphate, pH 6.5, VAPOR DIFFUSION/HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.0085
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0085 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. all: 281274 / Num. obs: 281274 / % possible obs: 99.8 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.3
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.31 / Num. unique all: 2687 / % possible all: 100
Reflection
*PLUS
Num. obs: 26568 / Num. measured all: 281274
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 2687 / Rmerge(I) obs: 0.31

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
RefinementResolution: 3→35 Å / Stereochemistry target values: Engh & Huber
Details: Least squares minimization of amplitudes using X-PLOR followed by maximum likelihood refinement of amplitudes using CNS
RfactorNum. reflection% reflection
Rfree0.307 816 -
Rwork0.267 --
all-26614 -
obs-18727 70.4 %
Refinement stepCycle: LAST / Resolution: 3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 154 0 6470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.623
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 35 Å / Rfactor obs: 0.267 / Rfactor Rfree: 0.304
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0092

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