SAXSdb — 6bxc

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

Toll-like receptor 5b, Variable lymphocyte receptor B chimera

Eptatretus burgeri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Variable Lymphocyte Receptor 9 (VLR9) × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2 其他Polymer 1	Variable Lymphocyte Receptor 9 (VLR9) × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F8W3J5_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–373； UniProt 28–396 Author chain B； PDBConstruct 5–373； UniProt 28–396

Toll-like receptor 5b, Variable lymphocyte receptor B chimera

Eptatretus burgeri

UniProt Q4G1L2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Variable Lymphocyte Receptor 9 (VLR9) × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2 其他Polymer 1	Variable Lymphocyte Receptor 9 (VLR9) × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4G1L2_EPTBU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 374–448； UniProt 126–200 Author chain B； PDBConstruct 374–448； UniProt 126–200

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	6bxc
Deposition date deposition_date	2017-12-18
Structure title title	Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 9 (VLR9) bound
Keywords keywords	VLR, LEUCINE-RICH REPEAT, antibody, 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.

6bxc__assembly_1__model_1

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

Download this curve (.dat)

6bxc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6bxc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.77 Å
Rg (electron density)	27.63 Å
Total Rg	28.40 Å
Atom count	4678
Residues	607
Excluded volume	83597 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6bxc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6bxc__assembly_2__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	Toll-like receptor 5b, Variable lymphocyte receptor B chimera
Molecular weight formula_weight	51169.2 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	9515

ADPGTSECSVIGYNAICINRGLHQVPELPAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGKHFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSYNHIRALGDQSFLGLPNLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPTSASLVPR

Source Source

Source organism organism	Eptatretus burgeri
Common name common_name	Inshore hagfish
NCBI taxonomy ID ncbi_taxonomy_id	7764
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Variable Lymphocyte Receptor 9 (VLR9)
Molecular weight formula_weight	19287.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GGHHHHHHGSENLYFQGACPSQCSCSGTTVDCSGKSLASVPGGIPTTTQVLYLYDNQITKLEPGVFDRLVNLQQLWLEINQLTSLPAGVFDNLTQLSILNMHTNQLKSIPRGAFDNLKSLTHIWLLNNPWDCACSDILYLSGWLGQHAGKEQGQAVCSGTNTPVRAVTEASTSPSKCP

Source Source

Source organism organism	Petromyzon marinus
Common name common_name	sea lamprey
NCBI taxonomy ID ncbi_taxonomy_id	7757
Host organism 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 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	3

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	121

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Unit-cell length a length_a	69.380 Å
Unit-cell length b length_b	69.413 Å
Unit-cell length c length_c	84.561 Å
Unit-cell angle α angle_alpha	112.14 °
Unit-cell angle β angle_beta	104.12 °
Unit-cell angle γ angle_gamma	100.81 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	45.272 Å
R factor r_factor	0.2315
R_work r_work	0.2295
R_free r_free	0.2703

Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 9 (VLR9) bound

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

Toll-like receptor 5b, Variable lymphocyte receptor B chimera

State in the Current Structure

Other States of the Same Protein in the Database

Toll-like receptor 5b, Variable lymphocyte receptor B chimera

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

6bxc__assembly_1__model_1

6bxc__assembly_1__model_1 | I(q)

6bxc__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 9 (VLR9) bound

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

Toll-like receptor 5b, Variable lymphocyte receptor B chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Toll-like receptor 5b, Variable lymphocyte receptor B chimera

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

6bxc__assembly_1__model_1

6bxc__assembly_1__model_1 | I(q)

6bxc__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)