SAXSdb — 8j6f

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

Interleukin-6 receptor subunit alpha

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	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 122–131 Chain I； UniProt 1–365	Not recorded	Heavy chain of Tocilizumab Fab × 1 Light chain of Tocilizumab Fab × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.30 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 8J6F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1N26 Crystal Structure of the extra-cellular domains of Human Interleukin-6 Receptor alpha chain Deposited 2002-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–344（325 aa） Fragment：IL-6R extral-cellular domains	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 4 CYS CYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；ammonium sulphate, PEG 3350, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.40 Å R-free 0.290
1P9M Crystal structure of the hexameric human IL-6/IL-6 alpha receptor/gp130 complex Deposited 2003-05-12	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 × 6 PDB declaration: hexameric	Chain C 115–315（201 aa） Fragment：extracellular domains D2 - D3	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；Sodium formate, Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.65 Å R-free 0.334
2ARW The solution structure of the membrane proximal cytokine receptor domain of the human interleukin-6 receptor Deposited 2005-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 212–336（125 aa） Fragment：Third extracellular domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；293 K；Ionic strength (raw mmCIF value) 50mM phosphate；Pressure ambient NMR sample composition 20mM phosphatebuffer pH 5.0, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
5FUC Biophysical and cellular characterisation of a junctional epitope antibody that locks IL-6 and gp80 together in a stable complex: implications for new therapeutic strategies Deposited 2016-01-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 111–322（212 aa） Fragment：RESIDUES 20-33 AND RESIDUES 111-322	Mutation：YES	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M MES, PH 6.5, 14% PEG20K	Resolution 2.70 Å R-free 0.287
5FUC Biophysical and cellular characterisation of a junctional epitope antibody that locks IL-6 and gp80 together in a stable complex: implications for new therapeutic strategies Deposited 2016-01-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 111–322（212 aa） Fragment：RESIDUES 20-33 AND RESIDUES 111-322	Mutation：YES	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M MES, PH 6.5, 14% PEG20K	Resolution 2.70 Å R-free 0.287
7DC8 Crystal structure of Switch Ab Fab and hIL6R in complex with ATP Deposited 2020-10-23	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 × 3 PDB declaration: trimeric	Chain C 111–320（210 aa）	Mutation：C193S	SO4 SULFATE ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.06 M Tris, 12.0 %(w/v) Polyethylene glycol 1500, 0.06 M Ammonium sulfate	Resolution 2.76 Å R-free 0.278
7DC8 Crystal structure of Switch Ab Fab and hIL6R in complex with ATP Deposited 2020-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 111–320（210 aa）	Mutation：C193S	SO4 SULFATE ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.06 M Tris, 12.0 %(w/v) Polyethylene glycol 1500, 0.06 M Ammonium sulfate	Resolution 2.76 Å R-free 0.278
8D82 Cryo-EM structure of human IL-6 signaling complex in detergent: model containing full extracellular domains Deposited 2022-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 20–331（312 aa） Chain G 20–331（312 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
8IOW Cryo-EM structure of the sarilumab Fab/IL-6R complex Deposited 2023-03-13	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D2 1–365（365 aa） Chain I 1–365（365 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8QY5 Structure of interleukin 6. Deposited 2023-10-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–468（468 aa） Chain F 1–468（468 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QY6 Structure of interleukin 6 (gp130 P496L mutant). Deposited 2023-10-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–468（468 aa） Chain F 1–468（468 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IL6RA_HUMAN
Isoform	P08887-2
PDB entities	3, 4
Chains and sequence ranges	Author chain I； PDBConstruct 1–365； UniProt 1–365 Author chain B； PDBConstruct 1–10； UniProt 122–131

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	8j6f
Deposition date deposition_date	2023-04-25
Structure title title	Cryo-EM structure of the Tocilizumab Fab/IL-6R complex
Keywords keywords	antibody, IL-6R, structural protein, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	27.09 Å
Radius of gyration Rg (electron density) rg_electron	26.66 Å
Forward intensity I(0) i0	50213400.00
Molecular weight molecular_weight	54863.0 kDa
Excluded volume excluded_volume	68446 Å³
Envelope volume envelope_volume	84865 Å³
Hydration-shell volume shell_volume	27537 Å³
Envelope diameter envelope_diameter	99.8 Å
Shell Rg shell_rg	32.96 Å
Envelope Rg envelope_rg	26.94 Å
Shape Rg shape_rg	26.66 Å
Total Rg total_rg	27.32 Å
Total atoms total_atoms	3870
Residues n_residues	496
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	95.5 Å
Rg (real space) rg_real	27.25 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	5.0210e+07
I(0) uncertainty (real space) i0_real_error	7.5660e+05
Rg (reciprocal space) rg_reciprocal	27.20 Å
I(0) (reciprocal space) i0_reciprocal	50210000.0000
Solution quality estimate total_estimate	0.8444
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.518
Kurtosis Kurtosis kurtosis	-0.134
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13740000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.794; Smooth: 0.938

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Heavy chain of Tocilizumab Fab
Molecular weight formula_weight	24125.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	3870

QVQLQESGPGLVRPSQTLSLTCTVSGYSITSDHAWSWVRQPPGRGLEWIGYISYSGITTYNPSLKSRVTMLRDTSKNQFSLRLSSVTAADTAVYYCARSLARTTAMDYWGQGSLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Light chain of Tocilizumab Fab
Molecular weight formula_weight	23527.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPSSLSASVGDRVTITCRASQDISSYLNWYQQKPGKAPKLLIYYTSRLHSGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQGNTLPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Interleukin-6 receptor subunit alpha
Molecular weight formula_weight	40283.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MLAVGCALLAALLAAPGAALAPRRCPAQEVARGVLTSLPGDSVTLTCPGVEPEDNATVHWVLRKPAAGSHPSRWAGMGRRLLLRSVQLHDSGNYSCYRAGRPAGTVHLLVDVPPEEPQLSCFRKSPLSNVVCEWGPRSTPSLTTKAVLLVRKFQNSPAEDFQEPCQYSQESQKFSCQLAVPEGDSSFYIVSMCVASSVGSKFSKTQTFQGCGILQPDPPANITVTAVARNPRWLSVTWQDPHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHCVIHDAWSGLRHVVQLRAQEEFGQGEWSEWSPEAMGTPWTESRSPPAENEVSTPMQALTTNKDDDNILFRDSANATSLPGSRRRGSCGL

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	Homo sapiens

Entity 4 Entity 4 polymer

Description description	IL6R-D2 peptide
Molecular weight formula_weight	1148.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

FRKSPLSNVV

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	Homo sapiens

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	351599

fit	/app/data/saxs_computation/j6/8j6f/8j6f.fit
pddf	/app/data/pr_computation/j6/8j6f/8j6f.pr.out
profile	/app/data/saxs_computation/j6/8j6f/8j6f.dat

Cryo-EM structure of the Tocilizumab Fab/IL-6R complex

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

Interleukin-6 receptor subunit alpha

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)