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

Method: X-RAY DIFFRACTION

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

INTERLEUKIN-6

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR × 1 （D6R9R8,P08887） VHH6 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR × 1 （D6R9R8,P08887） VHH6 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IL6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–166； UniProt 49–212 Author chain B； PDBConstruct 3–166； UniProt 49–212

INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR

HOMO SAPIENS

UniProt D6R9R8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	INTERLEUKIN-6 × 1 （P05231） VHH6 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	INTERLEUKIN-6 × 1 （P05231） VHH6 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D6R9R8_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–15； UniProt 20–33 Author chain D； PDBConstruct 2–15； UniProt 20–33

INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR

HOMO SAPIENS

UniProt P08887

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	INTERLEUKIN-6 × 1 （P05231） VHH6 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	INTERLEUKIN-6 × 1 （P05231） VHH6 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IL6RA_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 20–231； UniProt 111–322 Author chain D； PDBConstruct 20–231； UniProt 111–322

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	5fuc
Deposition date deposition_date	2016-01-25
Structure title title	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
Keywords keywords	VHH, IL-6, IL-6 RECEPTOR ALPHA, IL-6 RECEPTOR BETA, GP80, ANTIBODY, JUNCTIONAL EPITOPE, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5fuc__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5fuc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5fuc__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	26.97 Å
Rg (electron density)	26.21 Å
Total Rg	26.99 Å
Atom count	3777
Residues	474
Excluded volume	66636 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5fuc__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5fuc__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	INTERLEUKIN-6
Molecular weight formula_weight	18982.7 kDa
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	7672

GSSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR
Molecular weight formula_weight	25973.1 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GLAPRRCPAQEVARGAGAGDVPPEEPQLSCFRKSPLSNVVCEWGPRSTPSLTTKAVLLVRKFQNSPAEDFQEPCQYSQESQKFSCQLAVPEGDSSFYIVSMCVASSVGSKFSKTQTFQGAGILQPDPPANITVTAVARNPRWLSVTWQDPHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHAVIHDAWSGLRHVVQLRAQEEFGQGEWSEWSPEAMGTPWTESRSPP

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	HOMO SAPIENS

Entity 3 Entity 3 polymer

Description description	VHH6
Molecular weight formula_weight	14677.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,V

DVQFVESGGGSVHAGGSLRLNCATSGYIYSTYCMGWFRQAPGKEREGVAHIYTNSGRTYYADSVKGRFTISQDNAKNTVYLQMNSLKPEDTAIYYCAARPSIRCASFSATEYKDWGQGTQVTVSSRENLYFQ

Source Source

Source organism organism	CAMELUS DROMEDARIUS
Common name common_name	CAMEL
NCBI taxonomy ID ncbi_taxonomy_id	9838
Host organism host_organism	HOMO SAPIENS

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	111

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d5fuca1
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	d5fuca2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5fucb_
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	d5fucc1
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	d5fucc2
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	d5fucd1
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	d5fucd2
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	d5fuce_
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.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5fucv_
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.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (8 domains)

Domain ID domain_id	5fucA00
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	5fucB00
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	5fucC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5fucC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5fucD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5fucD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5fucE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5fucV00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	249.030 Å
Unit-cell length b length_b	67.800 Å
Unit-cell length c length_c	78.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2313
R_work r_work	0.2313
R_free r_free	0.2872

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

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

INTERLEUKIN-6

State in the Current Structure

Other States of the Same Protein in the Database

INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR

State in the Current Structure

Other States of the Same Protein in the Database

INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5fuc__assembly_1__model_1

5fuc__assembly_1__model_1 | I(q)

5fuc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)

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

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

INTERLEUKIN-6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5fuc__assembly_1__model_1

5fuc__assembly_1__model_1 | I(q)

5fuc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)