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- PDB-4rs1: Crystal structure of receptor-cytokine complex -

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Basic information

Entry
Database: PDB / ID: 4rs1
TitleCrystal structure of receptor-cytokine complex
Components
  • Granulocyte-macrophage colony-stimulating factor
  • Granulocyte-macrophage colony-stimulating factor receptor subunit alpha
KeywordsCYTOKINE RECEPTOR/CYTOKINE / CYTOKINE / RECEPTOR / CYTOKINE RECEPTOR-CYTOKINE COMPLEX
Function / homology
Function and homology information


growth hormone receptor activity / granulocyte macrophage colony-stimulating factor receptor binding / growth hormone receptor complex / histamine secretion / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / response to silicon dioxide / neutrophil differentiation / epithelial fluid transport / positive regulation of interleukin-23 production ...growth hormone receptor activity / granulocyte macrophage colony-stimulating factor receptor binding / growth hormone receptor complex / histamine secretion / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / response to silicon dioxide / neutrophil differentiation / epithelial fluid transport / positive regulation of interleukin-23 production / regulation of circadian sleep/wake cycle, sleep / dendritic cell differentiation / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / positive regulation of leukocyte proliferation / response to fluid shear stress / Surfactant metabolism / myeloid dendritic cell differentiation / myeloid cell differentiation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of macrophage derived foam cell differentiation / cell surface receptor signaling pathway via STAT / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of podosome assembly / growth hormone receptor signaling pathway / cytokine binding / Interleukin-10 signaling / peptide hormone binding / macrophage differentiation / monocyte differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / cell surface receptor signaling pathway via JAK-STAT / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / embryonic placenta development / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / cytokine-mediated signaling pathway / signaling receptor activity / cellular response to lipopolysaccharide / RAF/MAP kinase cascade / cell population proliferation / immune response / positive regulation of cell migration / external side of plasma membrane / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor signature. / Granulocyte-macrophage colony-simulating factor (GM-CSF) / 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 ...IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor signature. / Granulocyte-macrophage colony-simulating factor (GM-CSF) / 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 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
Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsBroughton, S.E. / Parker, M.W. / Dhagat, U.
CitationJournal: Structure / Year: 2016
Title: Conformational Changes in the GM-CSF Receptor Suggest a Molecular Mechanism for Affinity Conversion and Receptor Signaling.
Authors: Broughton, S.E. / Hercus, T.R. / Nero, T.L. / Dottore, M. / McClure, B.J. / Dhagat, U. / Taing, H. / Gorman, M.A. / King-Scott, J. / Lopez, A.F. / Parker, M.W.
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Granulocyte-macrophage colony-stimulating factor receptor subunit alpha
A: Granulocyte-macrophage colony-stimulating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2785
Polymers45,7442
Non-polymers5353
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint0 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.801, 77.169, 117.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Granulocyte-macrophage colony-stimulating factor receptor subunit alpha / GM-CSF-R-alpha / GMCSFR-alpha / GMR-alpha / CDw116


Mass: 32872.992 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 35-315 / Mutation: N27Q, N35Q, N80Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2R, CSF2RA, CSF2RY / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P15509
#2: Protein Granulocyte-macrophage colony-stimulating factor / GM-CSF / Colony-stimulating factor / CSF / Molgramostin / Sargramostim


Mass: 12870.766 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2, GMCSF / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04141
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 22% PEG8000, 1% MPD, 5MM DITHIOTHREITOL, 100MM IMIDAZOLE, PH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95443
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2009 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95443 Å / Relative weight: 1
ReflectionResolution: 2.68→46.805 Å / Num. obs: 13058 / % possible obs: 98.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8
Reflection shellResolution: 2.68→2.78 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→38.02 Å / SU ML: 0.44 / σ(F): 1.35 / Phase error: 31.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 642 4.92 %
Rwork0.225 --
obs0.228 13058 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.24 Å2
Refinement stepCycle: LAST / Resolution: 2.68→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 34 20 3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013144
X-RAY DIFFRACTIONf_angle_d1.4094237
X-RAY DIFFRACTIONf_dihedral_angle_d17.3761180
X-RAY DIFFRACTIONf_chiral_restr0.094466
X-RAY DIFFRACTIONf_plane_restr0.005544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.88730.40141290.32152258X-RAY DIFFRACTION92
2.8873-3.17770.34081390.28262494X-RAY DIFFRACTION100
3.1777-3.63720.30621290.23712485X-RAY DIFFRACTION100
3.6372-4.58130.26431280.20762535X-RAY DIFFRACTION100
4.5813-38.02520.26231170.20672644X-RAY DIFFRACTION99
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)
11.9978-2.6865-0.67350.92580.34080.5433-0.13890.14491.5503-0.1168-0.1418-2.0092-0.46750.2499-0.3631.201-0.71480.0775-0.0224-0.00151.007129.0634-1.91-24.3085
23.3496-0.37960.25733.14571.52380.8199-0.23740.15890.9774-0.6704-0.64870.8343-0.2059-0.36770.55271.11920.75570.1841-0.2168-0.16070.769814.52741.5994-26.6018
35.7463-1.1764-0.03414.32911.04993.32090.73161.2569-0.4851-0.2782-0.24740.9885-0.2508-1.0272-0.040.45390.33710.12940.56710.04750.535120.216-13.3555-35.9827
44.4602-2.92791.75284.97490.49813.03260.22481.28571.5901-0.7983-0.2194-0.8555-1.27890.6190.25540.78810.1090.20280.58510.42060.571425.7036-4.0835-35.5839
54.0653.13211.35042.83811.17144.63750.3578-0.3667-0.2634-0.0730.10310.7833-0.3728-0.8014-0.170.35040.21360.01830.51350.03710.467418.7741-10.4232-31.9517
61.5962-0.081.01173.2922-1.20384.933-0.04920.91170.1932-0.6433-0.29250.20540.0059-0.64890.38890.60920.19930.08951.3940.02070.5644-0.7411-16.7942-43.0071
78.1909-0.98471.48085.5454-1.92753.9044-0.14130.2482-0.3930.18030.1467-0.13760.7186-0.9324-0.02170.4241-0.15630.09630.4606-0.16140.40175.3752-27.2532-17.2385
81.4404-0.5935-1.41341.10220.3614.6145-0.2532-0.0298-0.2609-0.05070.3172-0.2615-0.25780.3964-0.030.33790.01160.06730.1617-0.04470.278419.9081-18.6812-14.1329
91.6228-1.0468-0.73885.0521-2.46682.3752-0.1870.1605-0.34921.00920.8778-0.7988-2.2771.9403-0.33820.8086-0.35650.09980.963-0.16970.373836.3265-6.01541.4901
102.04980.6357-1.38814.87671.95362.21730.4395-1.4446-0.39881.9833-0.32050.201-0.7050.00090.01780.7380.30650.1482-0.6743-0.57670.198627.1572-11.8752-2.6156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 14:22)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 23:38)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 39:60)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 61:93)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 94:124)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 17:96)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 97:169)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 170:233)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 234:272)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 273:296)

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