SAXSdb — 5gy2

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

Tlr5b protein,Variable lymphocyte receptor B

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 其他Polymer 1	Flagellin × 1 （E0U497） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 TETRAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2 其他Polymer 1	Flagellin × 1 （E0U497） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 TETRAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B3DIN1_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–373； UniProt 23–390 Author chain B； PDBConstruct 6–373； UniProt 23–390

Tlr5b protein,Variable lymphocyte receptor B

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 其他Polymer 1	Flagellin × 1 （E0U497） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 TETRAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2 其他Polymer 1	Flagellin × 1 （E0U497） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 TETRAETHYLENE GLYCOL × 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

Flagellin

Bacillus subtilis subsp. spizizenii strain W23

UniProt E0U497

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2 其他Polymer 1	Tlr5b protein,Variable lymphocyte receptor B × 1 （B3DIN1,Q4G1L2） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 TETRAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2 其他Polymer 1	Tlr5b protein,Variable lymphocyte receptor B × 1 （B3DIN1,Q4G1L2） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 TETRAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E0U497_BACPZ
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 7–183； UniProt 54–230 Author chain D； PDBConstruct 7–183； UniProt 54–230

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	5gy2
Deposition date deposition_date	2016-09-21
Structure title title	Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5
Keywords keywords	Bacterial protein Immune receptor, 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.

5gy2__assembly_1__model_1

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

Download this curve (.dat)

5gy2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5gy2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.58 Å
Rg (electron density)	27.45 Å
Total Rg	28.23 Å
Atom count	4807
Residues	611
Excluded volume	85497 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5gy2__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5gy2__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	Tlr5b protein,Variable lymphocyte receptor B
Molecular weight formula_weight	51169.2 kDa
Mutation mutation	V24E/L124V/Q159K/R227K/S229T/D334N
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	10156

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Flagellin
Molecular weight formula_weight	19254.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSAKDPGQIRGLEMASKNSQDGISLIQTAEGALTETHAILQRMRELTVQAGNTGTQQAEDLGAIKDEMDALIEEIDGISNRTEFNGKKLLDGTNSTDGFTFQIGANAGQQLNVKIDSMSSTALGVNALDVTDFAATAFDDQLKSIDTAINTVSTQRAKLGAVQNRLEHTINNLGASGENLTAA

Source Source

Source organism organism	Bacillus subtilis subsp. spizizenii strain W23
NCBI taxonomy ID ncbi_taxonomy_id	655816
Host organism host_organism	Escherichia coli

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	2

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	6

Entity 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	465

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5gy2C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1330 — f41 fragment of flagellin, N-terminal domain
Homologous superfamily homologous superfamily	10 — f41 fragment of flagellin, N-terminal domain

Domain ID domain_id	5gy2D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1330 — f41 fragment of flagellin, N-terminal domain
Homologous superfamily homologous superfamily	10 — f41 fragment of flagellin, N-terminal domain

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Unit-cell length a length_a	78.146 Å
Unit-cell length b length_b	54.281 Å
Unit-cell length c length_c	165.980 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1969
R_work r_work	0.1948
R_free r_free	0.2363

Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5

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

Tlr5b protein,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Tlr5b protein,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Flagellin

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

5gy2__assembly_1__model_1

5gy2__assembly_1__model_1 | I(q)

5gy2__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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5

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

Tlr5b protein,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tlr5b protein,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Flagellin

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

5gy2__assembly_1__model_1

5gy2__assembly_1__model_1 | I(q)

5gy2__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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)