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2gmf

HUMAN GRANULOCYTE MACROPHAGE COLONY STIMULATING FACTOR

Method: X-RAY DIFFRACTION Dmax: 71.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR

Homo sapiens

UniProt P04141

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 18–144 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 18–144 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2GMF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CSG Three-dimensional structure of recombinant human granulocyte-macrophage colony-stimulating factor Deposited 1992-11-23 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–144（127 aa）
Chain B 18–144（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
4NKQ Structure of a Cytokine Receptor Complex Deposited 2013-11-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 18–144（127 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；293 K；100mM HEPES buffer (pH 7.0), 6%(v/v) PEG3350, 0.2M proline, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.273
4RS1 Crystal structure of receptor-cytokine complex Deposited 2014-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 31–142（112 aa） Fragment：RESIDUES 31-142
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；22% PEG8000, 1% MPD, 5MM DITHIOTHREITOL, 100MM IMIDAZOLE, PH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.68 Å R-free 0.287
5C7X Crystal structure of MOR04357, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF Deposited 2015-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 18–144（127 aa） Fragment：UNP residues 18-144
Not recorded PGE TRIETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；100 mM sodium acetate, pH 4.0-4.3, 39-42 % (w/v) PEG 400, 40 mg/mL protein
Resolution 2.95 Å R-free 0.276
5C7X Crystal structure of MOR04357, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF Deposited 2015-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 18–144（127 aa） Fragment：UNP residues 18-144
Not recorded PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；100 mM sodium acetate, pH 4.0-4.3, 39-42 % (w/v) PEG 400, 40 mg/mL protein
Resolution 2.95 Å R-free 0.276
5D70 Crystal structure of MOR03929, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF Deposited 2015-08-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 18–144（127 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.75；293 K；100 mM Tris, pH 8.75, 200 mM LiSO4, 25-28 % (w/v) PEG 3350, 28mg/mL protein
Resolution 2.06 Å R-free 0.222
5D71 Crystal structure of MOR04302, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF Deposited 2015-08-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–127（127 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；100 mM sodium acetate, pH 4.0-4.3, 39-42 % (w/v) PEG 400, 35 mg/mL protein
Resolution 2.25 Å R-free 0.219
5D72 Crystal structure of MOR04252, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF Deposited 2015-08-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–127（127 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；100 mM sodium acetate, pH 4.0-4.3, 39-42 % (w/v) PEG 400, 30 mg/mL protein
Resolution 2.60 Å R-free 0.266
5D72 Crystal structure of MOR04252, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF Deposited 2015-08-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–127（127 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；100 mM sodium acetate, pH 4.0-4.3, 39-42 % (w/v) PEG 400, 30 mg/mL protein
Resolution 2.60 Å R-free 0.266
6BFQ The mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies Deposited 2017-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 18–144（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283.15 K；0.16 M Calcium acetate, 14.4% PEG8000, 0.08 M Sodium Cacodylate pH 6.5 and 20% glycerol
Resolution 2.60 Å R-free 0.264
6BFQ The mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies Deposited 2017-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 18–144（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283.15 K；0.16 M Calcium acetate, 14.4% PEG8000, 0.08 M Sodium Cacodylate pH 6.5 and 20% glycerol
Resolution 2.60 Å R-free 0.264
6BFQ The mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies Deposited 2017-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 18–144（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283.15 K；0.16 M Calcium acetate, 14.4% PEG8000, 0.08 M Sodium Cacodylate pH 6.5 and 20% glycerol
Resolution 2.60 Å R-free 0.264
6BFQ The mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies Deposited 2017-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 18–144（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283.15 K；0.16 M Calcium acetate, 14.4% PEG8000, 0.08 M Sodium Cacodylate pH 6.5 and 20% glycerol
Resolution 2.60 Å R-free 0.264
6BFS The mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies Deposited 2017-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 18–144（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283.15 K；0. 2 M Sodium Chloride, 20% PEG 8000, 0.1 M phosphate Citrate 4.5
Resolution 2.00 Å R-free 0.248
9JKR human GM-CSF with Fabs from autoantibodies, F1 and C. Deposited 2024-09-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 18–144（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

10 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSF2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–127； UniProt 18–144 Author chain B； PDBConstruct 1–127； UniProt 18–144

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2gmf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2gmf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2gmf
Deposition date deposition_date1996-04-24
Structure title titleHUMAN GRANULOCYTE MACROPHAGE COLONY STIMULATING FACTOR
Keywords keywordsGRANULOCYTE-MACROPHAGE COLONY STIMULATING GROWTH FACTOR, GROWTH FACTOR; GROWTH FACTOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.28 Å
Radius of gyration Rg (electron density) rg_electron21.41 Å
Forward intensity I(0) i013814900.00
Molecular weight molecular_weight27625.0 kDa
Excluded volume excluded_volume34471 ų
Envelope volume envelope_volume42704 ų
Hydration-shell volume shell_volume17416 ų
Envelope diameter envelope_diameter71.7 Å
Shell Rg shell_rg26.71 Å
Envelope Rg envelope_rg21.45 Å
Shape Rg shape_rg21.41 Å
Total Rg total_rg22.17 Å
Total atoms total_atoms1935
Residues n_residues241
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax71.8 Å
Rg (real space) rg_real22.30 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real1.3810e+07
I(0) uncertainty (real space) i0_real_error1.6830e+05
Rg (reciprocal space) rg_reciprocal22.30 Å
I(0) (reciprocal space) i0_reciprocal13810000.0000
Solution quality estimate total_estimate0.9052
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.8 Å
Skewness Skewness skewness0.302
Kurtosis Kurtosis kurtosis-0.548
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha2232000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.986
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2gmfa1
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.2 — Short-chain cytokines
Domain ID domain_idd2gmfa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2gmfb1
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.2 — Short-chain cytokines
Domain ID domain_idd2gmfb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id2gmfA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
Domain ID domain_id2gmfB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
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8. Citations (3)

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9. Files and Curves (10)