SAXSdb — 2d9q

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1. Protein Identity and Related Structures Protein Identity & Related Structures

CSF3

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 31–204	Fragment：residues 1-174	Granulocyte colony-stimulating factor receptor × 2 （Q99062） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	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

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 2D9Q	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 oligomeric state 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
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 40–202（163 aa） Fragment：UNP residues 40-202 Chain C 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 40–202（163 aa） Fragment：UNP residues 40-202 Chain D 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5ZO6 Crystal structure of C166, a backbone circularized G-CSF Deposited 2018-04-12	Different construct Different mutation/modification Different oligomeric state 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 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSF3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–174； UniProt 31–204

Granulocyte colony-stimulating factor receptor

Homo sapiens

UniProt Q99062

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 25–332	Fragment：Ig-CRH DOMAIN Mutation：C79S, C164S, C229S	CSF3 × 2 （P09919） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CSF3R_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–308； UniProt 25–332

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2d9q
Deposition date deposition_date	2005-12-12
Structure title title	Crystal Structure of the Human GCSF-Receptor Signaling Complex
Keywords keywords	CYTOKINE, LIGAND-RECEPTOR COMPLEX, SIGNALING PROTEIN-CYTOKINE COMPLEX; SIGNALING PROTEIN/CYTOKINE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	34.01 Å
Radius of gyration Rg (electron density) rg_electron	34.01 Å
Forward intensity I(0) i0	43725100.00
Molecular weight molecular_weight	51791.0 kDa
Excluded volume excluded_volume	64833 Å³
Envelope volume envelope_volume	90230 Å³
Hydration-shell volume shell_volume	25171 Å³
Envelope diameter envelope_diameter	119.0 Å
Shell Rg shell_rg	35.26 Å
Envelope Rg envelope_rg	34.87 Å
Shape Rg shape_rg	34.02 Å
Total Rg total_rg	34.09 Å
Total atoms total_atoms	3633
Residues n_residues	467
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	114.8 Å
Rg (real space) rg_real	34.40 Å
Rg uncertainty (real space) rg_real_error	1.20 Å
I(0) (real space) i0_real	4.3730e+07
I(0) uncertainty (real space) i0_real_error	7.3630e+05
Rg (reciprocal space) rg_reciprocal	34.16 Å
I(0) (reciprocal space) i0_reciprocal	43720000.0000
Solution quality estimate total_estimate	0.7783
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.3 Å
Skewness Skewness skewness	0.522
Kurtosis Kurtosis kurtosis	-0.558
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3254000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.693; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.431; Smooth: 0.605

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	CSF3
Molecular weight formula_weight	18685.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3647

TPLGPASSLPQSFLLKCLEQVRKIQGDGAALQEKLCATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQLAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEELGMAPALQPTQGAMPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLAQP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Granulocyte colony-stimulating factor receptor
Molecular weight formula_weight	34709.7 kDa
Mutation mutation	C79S, C164S, C229S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ECGHISVSAPIVHLGDPITASCIIKQNCSHLDPEPQILWRLGAELQPGGRQQRLSDGTQESIITLPHLNHTQAFLSCSLNWGNSLQILDQVELRAGYPPAIPHNLSCLMNLTTSSLICQWEPGPETHLPTSFTLKSFKSRGNCQTQGDSILDCVPKDGQSHCSIPRKHLLLYQNMGIWVQAENALGTSMSPQLCLDPMDVVKLEPPMLRTMDPSPEAAPPQAGCLQLSWEPWQPGLHINQKCELRHKPQRGEASWALVGPLPLEALQYELCGLLPATAYTLQIRCIRWPLPGHWSDWSPSLELRTTERAAAPR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2d9qa_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.1 — Long-chain cytokines

Domain ID domain_id	d2d9qb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.3 — C2 set domains

Domain ID domain_id	d2d9qb2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d2d9qb3
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

CATH v4.4 (4 domains)

Domain ID domain_id	2d9qA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2d9qB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2d9qB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2d9qB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (3)

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Unit-cell length a length_a	134.777 Å
Unit-cell length b length_b	134.777 Å
Unit-cell length c length_c	105.468 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2531
R_work r_work	0.2515
R_free r_free	0.2844

fit	/app/data/saxs_computation/d9/2d9q/2d9q.fit
pddf	/app/data/pr_computation/d9/2d9q/2d9q.pr.out
profile	/app/data/saxs_computation/d9/2d9q/2d9q.dat

Crystal Structure of the Human GCSF-Receptor Signaling Complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

CSF3

State in the Current Structure

Other States of the Same Protein in the Database

Granulocyte colony-stimulating factor receptor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)