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- PDB-2gmf: HUMAN GRANULOCYTE MACROPHAGE COLONY STIMULATING FACTOR -

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Basic information

Entry
Database: PDB / ID: 2gmf
TitleHUMAN GRANULOCYTE MACROPHAGE COLONY STIMULATING FACTOR
ComponentsGRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR
KeywordsGROWTH FACTOR / GRANULOCYTE-MACROPHAGE COLONY STIMULATING GROWTH FACTOR
Function / homology
Function and homology information


granulocyte macrophage colony-stimulating factor receptor binding / histamine secretion / 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 ...granulocyte macrophage colony-stimulating factor receptor binding / histamine secretion / 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 / 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 / Interleukin-10 signaling / 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 / growth factor activity / cellular response to lipopolysaccharide / RAF/MAP kinase cascade / cell population proliferation / immune response / positive regulation of cell migration / 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
Similarity search - Function
Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor signature. / Granulocyte-macrophage colony-simulating factor (GM-CSF) / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Granulocyte-macrophage colony-stimulating factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsRozwarski, D. / Diederichs, K. / Hecht, R. / Boone, T. / Karplus, P.A.
Citation
Journal: Proteins / Year: 1996
Title: Refined crystal structure and mutagenesis of human granulocyte-macrophage colony-stimulating factor.
Authors: Rozwarski, D.A. / Diederichs, K. / Hecht, R. / Boone, T. / Karplus, P.A.
#1: Journal: Science / Year: 1991
Title: Novel Fold and Putative Receptor Binding Site of Granulocyte-Macrophage Colony-Stimulating Factor
Authors: Diederichs, K. / Boone, T. / Karplus, P.A.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Low-Resolution Structure of Recombinant Human Granulocyte-Macrophage Colony Stimulating Factor
Authors: Diederichs, K. / Jacques, S. / Boone, T. / Karplus, P.A.
History
DepositionApr 24, 1996Processing site: BNL
SupersessionNov 8, 1996ID: 1GMF
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR
B: GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR


Theoretical massNumber of molelcules
Total (without water)28,9852
Polymers28,9852
Non-polymers00
Water1,65792
1
A: GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR


Theoretical massNumber of molelcules
Total (without water)14,4921
Polymers14,4921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR


Theoretical massNumber of molelcules
Total (without water)14,4921
Polymers14,4921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.520, 59.060, 126.290
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 GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR


Mass: 14492.495 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04141
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.5 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
22 mMpotassium phosphate1drop
321 %(w/v)PEG80001reservoir
40.2 Msodium citrate/phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.4→10 Å / σ(F): 0
Details: PRO A 124 IS VERY MOBILE. THE PEPTIDE BOND PRECEDING IT IS NOT RELIABLY REFINED. PRO A 124 IS VERY MOBILE. THE PEPTIDE BOND PRECEDING IT IS NOT RELIABLY REFINED.
RfactorNum. reflection
Rwork0.235 -
obs0.235 19868
Displacement parametersBiso mean: 40 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 0 92 2029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.5
X-RAY DIFFRACTIONx_improper_angle_deg

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