5GY2: Tlr5b protein,Variable lymphocyte receptor B

Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5. Determined by X-ray diffraction at 2.1 Å resolution. Released 15 Feb 2017.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Danio rerio, Eptatretus burgeri, Bacillus subtilis subsp. spizizenii strain W23
Chains: 4
Atoms: 10,156
Mol. weight: 143.41 kDa
Ligands: NAG
Released: 15 Feb 2017

Explore 5GY2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5GY2 contains 28 α-helices and 74 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	1
β-strand	31-33	3	1
α-helix	42-44	3
β-strand	51-53	3	1
β-strand	61-62	2	2
β-strand	75-77	3	1
β-strand	86-87	2	2
β-strand	100-102	3	1
β-strand	110-111	2	2
β-strand	124-126	3	1
β-strand	133	1	3
α-helix	135-138	4
β-strand	150-152	3	1
β-strand	157	1	3
α-helix	165-169	5
β-strand	175-177	3	1
β-strand	183	1	4
α-helix	192-194	3
β-strand	198-203	6	1
β-strand	208	1	4
α-helix	217-220	4
β-strand	230-235	6	1
α-helix	243-252	10
β-strand	257-262	6	1
α-helix	279-281	3
α-helix	287-291	5
β-strand	296-298	3	1
β-strand	306-307	2	5
β-strand	320-322	3	1
β-strand	330-331	2	5
β-strand	344-346	3	1
β-strand	355	1	6
β-strand	368-370	3	1
β-strand	379	1	6
β-strand	392-394	3	1
β-strand	416-418	3	1
β-strand	424	1	7
α-helix	432-440	9
β-strand	445	1	1
β-strand	450	1	8
β-strand	451	1	7
β-strand	457	1	8
α-helix	458-460	3

Chain B: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	11
β-strand	31-33	3	11
α-helix	42-44	3
β-strand	51-53	3	11
β-strand	61-62	2	12
β-strand	75-77	3	11
β-strand	86-87	2	12
β-strand	100-102	3	11
β-strand	110-111	2	12
β-strand	124-126	3	11
β-strand	133	1	13
α-helix	135-138	4
β-strand	150-152	3	11
β-strand	157	1	13
α-helix	165-169	5
β-strand	175-177	3	11
β-strand	183	1	14
α-helix	192-194	3
β-strand	198-203	6	11
β-strand	208	1	14
α-helix	217-221	5
β-strand	230-235	6	11
α-helix	243-252	10
β-strand	257-262	6	11
α-helix	279-281	3
α-helix	287-291	5
β-strand	296-298	3	11
β-strand	306-307	2	15
β-strand	320-322	3	11
β-strand	330-331	2	15
β-strand	344-346	3	11
β-strand	355	1	16
β-strand	368-370	3	11
β-strand	379	1	16
β-strand	392-394	3	11
β-strand	416-418	3	11
β-strand	424	1	17
α-helix	432-440	9
β-strand	445	1	11
β-strand	450	1	18
β-strand	451	1	17
β-strand	457	1	18
α-helix	458-460	3

Chains C and D: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	55-98	44
α-helix	107-128	22
β-strand	130-131	2	9
β-strand	134-135	2	9
β-strand	146-149	4	10
β-strand	157-160	4	10
α-helix	167-170	4
α-helix	185-221	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tlr5b protein,Variable lymphocyte receptor B	A, B	protein	455	Danio rerio, Eptatretus burgeri	B3DIN1 (AlphaFold model), Q4G1L2 (AlphaFold model)
Flagellin	C, D	protein	183	Bacillus subtilis subsp. spizizenii strain W23	E0U497 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5GY2_1 Tlr5b protein,Variable lymphocyte receptor B (chains A, B)
ADPGTSECSVIGYNAICINRGLHQVPELPAHVNYVDLSLNSIAELNETSFSRLQDLQFLK
VEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVL
SGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGK
HFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAKRFFDAIAGTK
IQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTD
LEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSYNHIR
ALGDQSFLGLPNLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW
LNKNSQKEQGSAKCSGSGKPVRSIICPTSASLVPR

Sequence of entity 2 (C, D), FASTA

>5GY2_2 Flagellin (chains C, D)
GSAKDPGQIRGLEMASKNSQDGISLIQTAEGALTETHAILQRMRELTVQAGNTGTQQAED
LGAIKDEMDALIEEIDGISNRTEFNGKKLLDGTNSTDGFTFQIGANAGQQLNVKIDSMSS
TALGVNALDVTDFAATAFDDQLKSIDTAINTVSTQRAKLGAVQNRLEHTINNLGASGENL
TAA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Water and common crystallization additives (PG4) are not listed.

Primary citation

A conserved TLR5 binding and activation hot spot on flagellin. Song, W.S., Jeon, Y.J., Namgung, B. et al. Sci Rep (2017) 7:40878-40878. DOI 10.1038/srep40878 · PubMed

Other PDB entries of the same protein (UniProt B3DIN1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V47 2.47 Å, Crystal structure of the N-terminal fragment of zebrafish TLR5 in complex with…
3V44 2.83 Å, Crystal structure of the N-terminal fragment of zebrafish TLR5

Browse structure collections

About this viewer

MolViewer shows 5GY2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.