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5gw9

Crystal structure of C163, a backbone circularized G-CSF

Method: X-RAY DIFFRACTION Dmax: 89.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Granulocyte colony-stimulating factor

Homo sapiens

UniProt P09919

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 40–202 Fragment：UNP residues 40-202 Mutation：P40S, C47S, A205G No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；0.4M Ammonium sulfate Resolution 1.65 Å R-free 0.218
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 40–202 Fragment：UNP residues 40-202 Mutation：P40S, C47S, A205G No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；0.4M Ammonium sulfate Resolution 1.65 Å R-free 0.218
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 40–202 Fragment：UNP residues 40-202 Mutation：P40S, C47S, A205G No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；0.4M Ammonium sulfate Resolution 1.65 Å R-free 0.218
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 40–202 Fragment：UNP residues 40-202 Mutation：P40S, C47S, A205G No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；0.4M Ammonium sulfate Resolution 1.65 Å R-free 0.218
5 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 40–202 Chain C； UniProt 40–202 Fragment：UNP residues 40-202 Mutation：P40S, C47S, A205G No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；0.4M Ammonium sulfate Resolution 1.65 Å R-free 0.218
6 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 40–202 Chain D； UniProt 40–202 Fragment：UNP residues 40-202 Mutation：P40S, C47S, A205G No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；0.4M Ammonium sulfate Resolution 1.65 Å R-free 0.218

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 5GW9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CD9 2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR Deposited 1999-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 13–186（174 aa）
Chain C 13–186（174 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.80 Å R-free 0.319
1GNC STRUCTURE AND DYNAMICS OF THE HUMAN GRANULOCYTE COLONY-STIMULATING FACTOR DETERMINED BY NMR SPECTROSCOPY. LOOP MOBILITY IN A FOUR-HELIX-BUNDLE PROTEIN Deposited 1994-03-08 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–207（177 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1PGR 2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR Deposited 1999-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 13–186（174 aa）
Chain C 13–186（174 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 3.50 Å
1PGR 2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR Deposited 1999-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 13–186（174 aa）
Chain G 13–186（174 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 3.50 Å
1RHG THE STRUCTURE OF GRANULOCYTE-COLONY-STIMULATING FACTOR AND ITS RELATIONSHIP TO THOSE OF OTHER GROWTH FACTORS Deposited 1993-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 31–207（177 aa）
Chain B 31–207（177 aa）
Chain C 31–207（177 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
2D9Q Crystal Structure of the Human GCSF-Receptor Signaling Complex Deposited 2005-12-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 31–204（174 aa） Fragment：residues 1-174
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；0.2M ammonium phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.284
5ZO6 Crystal structure of C166, a backbone circularized G-CSF Deposited 2018-04-12 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 37–205（169 aa） Fragment：UNP residues 37-205
Mutation：C11S, A166G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；sodium acetate trihydrate, sodium chloride dehydrate, PEG 1500, MPD
Resolution 1.70 Å R-free 0.217

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSF3_HUMAN
Isoform P09919-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–163； UniProt 40–202 Author chain B； PDBConstruct 1–163； UniProt 40–202 Author chain C； PDBConstruct 1–163； UniProt 40–202 Author chain D； PDBConstruct 1–163； UniProt 40–202

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 5gw9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5gw9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5gw9
Deposition date deposition_date2016-09-09
Structure title titleCrystal structure of C163, a backbone circularized G-CSF
Keywords keywordscytokine, four-helix bundle, backbone circulatization; CYTOKINE
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_guinier28.85 Å
Radius of gyration Rg (electron density) rg_electron28.06 Å
Forward intensity I(0) i076723000.00
Molecular weight molecular_weight70245.0 kDa
Excluded volume excluded_volume88729 ų
Envelope volume envelope_volume109380 ų
Hydration-shell volume shell_volume32996 ų
Envelope diameter envelope_diameter93.8 Å
Shell Rg shell_rg34.82 Å
Envelope Rg envelope_rg27.96 Å
Shape Rg shape_rg28.04 Å
Total Rg total_rg28.82 Å
Total atoms total_atoms4940
Residues n_residues652
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 dmax89.1 Å
Rg (real space) rg_real28.79 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real7.6720e+07
I(0) uncertainty (real space) i0_real_error1.0030e+06
Rg (reciprocal space) rg_reciprocal28.82 Å
I(0) (reciprocal space) i0_reciprocal76720000.0000
Solution quality estimate total_estimate0.9043
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.6 Å
Skewness Skewness skewness0.246
Kurtosis Kurtosis kurtosis-0.466
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20530000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.871
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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5gw9a_
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.1 — Long-chain cytokines
Domain ID domain_idd5gw9b_
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.1 — Long-chain cytokines
Domain ID domain_idd5gw9c_
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.1 — Long-chain cytokines
Domain ID domain_idd5gw9d_
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.1 — Long-chain cytokines

CATH v4.4 (4 domains)

Domain ID domain_id5gw9A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5gw9B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5gw9C00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5gw9D00
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 (1)

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9. Files and Curves (10)