1gh7

CRYSTAL STRUCTURE OF THE COMPLETE EXTRACELLULAR DOMAIN OF THE BETA-COMMON RECEPTOR OF IL-3, IL-5, AND GM-CSF

Method: X-RAY DIFFRACTION D_max: 151.1 Å Quality: GOOD

▼

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

CYTOKINE RECEPTOR COMMON BETA CHAIN

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 Homooligomer Protein × 2 其他Polymer 4 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 25–437 Chain B； UniProt 25–437	Fragment：EXTRACELLULAR DOMAIN Mutation：N328Q	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG MME 5000, Phosphate, pH 6.5, VAPOR DIFFUSION/HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.307

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 1GH7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C8P NMR STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE COMMON BETA-CHAIN IN THE GM-CSF, IL-3 AND IL-5 RECEPTORS Deposited 1999-10-05	Different construct Different mutation/modification 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 338–438（101 aa） Fragment：DOMAIN 4	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；293 K；Ionic strength (raw mmCIF value) 0.06M；Pressure AMBIENT NMR sample composition 0.4MM D4BC U-15N; 10MM PHOSPHATE BUFFER;90% H2O, 10% D2O NMR sample composition 0.4MM D4BC U-15N; 10MM PHOSPHATE BUFFER;100% D2O	Resolution not provided
1EGJ DOMAIN 4 OF THE BETA COMMON CHAIN IN COMPLEX WITH AN ANTIBODY Deposited 2000-02-15	Different construct Different mutation/modification 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 338–438（101 aa） Fragment：DOMAIN 4	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；12% peg 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K	Resolution 2.80 Å R-free 0.288
2NA8 Transmembrane Structure of the Cytokine Receptor Common Subunit beta Deposited 2015-12-21	Different construct Different mutation/modification 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 432–473（42 aa） Fragment：Helical transmembrane residues 432-473	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；313 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N; 80% 2H] protein, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
2NA9 Transmembrane Structure of the P441A Mutant of the Cytokine Receptor Common Subunit beta Deposited 2015-12-21	Different construct Different mutation/modification 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 432–473（42 aa） Fragment：Helical transmembrane residues 432-473	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；313 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N; 80% 2H] protein, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
4NKQ Structure of a Cytokine Receptor Complex Deposited 2013-11-13	Different construct Different mutation/modification 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 25–438（414 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
5DWU Beta common receptor in complex with a Fab Deposited 2015-09-23	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 17–240（224 aa） Chain B 241–443（203 aa）	Mutation：N106Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M Tris 8, 25% - 35% PEG200	Resolution 3.97 Å R-free 0.330
6NMY A Cytokine-receptor complex Deposited 2019-01-13	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 25–240（216 aa） Chain B 241–438（198 aa）	Mutation：N346Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277.15 K；Crystals were grown in 10 mM Tris pH6.8, 8% PEG 8000, 0.15 M magnesium chloride	Resolution 3.30 Å R-free 0.278
6NMY A Cytokine-receptor complex Deposited 2019-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 25–240（216 aa） Chain D 241–438（198 aa）	Mutation：N346Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277.15 K；Crystals were grown in 10 mM Tris pH6.8, 8% PEG 8000, 0.15 M magnesium chloride	Resolution 3.30 Å R-free 0.278
8TLD Structure of the IL-5 Signaling Complex Deposited 2023-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 23–442（420 aa） Chain E 23–442（420 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYRB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–419； UniProt 25–437 Author chain B； PDBConstruct 1–419； UniProt 25–437

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1gh7
Deposition date deposition_date	2000-11-27
Structure title title	CRYSTAL STRUCTURE OF THE COMPLETE EXTRACELLULAR DOMAIN OF THE BETA-COMMON RECEPTOR OF IL-3, IL-5, AND GM-CSF
Keywords keywords	Dimer of interlocking chains of fibronectin-III domains Four fibronectin-III domains per chain, CYTOKINE RECEPTOR; CYTOKINE RECEPTOR
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	45.74 Å
Radius of gyration Rg (electron density) rg_electron	45.86 Å
Forward intensity I(0) i0	140880000.00
Molecular weight molecular_weight	91874.0 kDa
Excluded volume excluded_volume	112840 Å³
Envelope volume envelope_volume	189180 Å³
Hydration-shell volume shell_volume	36325 Å³
Envelope diameter envelope_diameter	151.5 Å
Shell Rg shell_rg	47.10 Å
Envelope Rg envelope_rg	44.61 Å
Shape Rg shape_rg	45.90 Å
Total Rg total_rg	45.80 Å
Total atoms total_atoms	6470
Residues n_residues	816
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

▼

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

Maximum dimension Dmax dmax	151.1 Å
Rg (real space) rg_real	46.10 Å
Rg uncertainty (real space) rg_real_error	2.16 Å
I(0) (real space) i0_real	1.4090e+08
I(0) uncertainty (real space) i0_real_error	2.6840e+06
Rg (reciprocal space) rg_reciprocal	45.74 Å
I(0) (reciprocal space) i0_reciprocal	140800000.0000
Solution quality estimate total_estimate	0.8213
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.297
Kurtosis Kurtosis kurtosis	-0.877
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5418000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.699; Smooth: 0.564

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CYTOKINE RECEPTOR COMMON BETA CHAIN
Molecular weight formula_weight	47812.5 kDa
Mutation mutation	N328Q
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6470

EETIPLQTLRCYNDYTSHITCRWADTQDAQRLVNVTLIRRVNEDLLEPVSCDLSDDMPWSACPHPRCVPRRCVIPCQSFVVTDVDYFSFQPDRPLGTRLTVTLTQHVQPPEPRDLQISTDQDHFLLTWSVALGSPQSHWLSPGDLEFEVVYKRLQDSWEDAAILLSNTSQATLGPEHLMPSSTYVARVRTRLAPGSRLSGRPSKWSPEVCWDSQPGDEAQPQNLECFFDGAAVLSCSWEVRKEVASSVSFGLFYKPSPDAGSAVLLREEECSPVLREGLGSLHTRHHCQIPVPDPATHGQYIVSVQPRRAEKHIKSSVNIQMAPPSLQVTKDGDSYSLRWETMKMRYEHIDHTFEIQYRKDTATWKDSKTETLQNAHSMALPALEPSTRYWARVRVRTSRTGYNGIWSEWSEARSWDTE

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	Trichoplusia ni

Entity 2 Entity 2 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	2

▼

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1gh7a1
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	d1gh7a2
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	d1gh7a3
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	d1gh7a4
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	d1gh7b1
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	d1gh7b2
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	d1gh7b3
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	d1gh7b4
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 (8 domains)

Domain ID domain_id	1gh7A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1gh7A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1gh7A03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1gh7A04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1gh7B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1gh7B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1gh7B03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1gh7B04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	185.700 Å
Unit-cell length b length_b	185.700 Å
Unit-cell length c length_c	103.300 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	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	—
R_work r_work	0.2670
R_free r_free	0.3070

fit	/app/data/saxs_computation/gh/1gh7/1gh7.fit
pddf	/app/data/pr_computation/gh/1gh7/1gh7.pr.out
profile	/app/data/saxs_computation/gh/1gh7/1gh7.dat