6BXC: PDB entry 6BXC

Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 9 (VLR9) bound. Determined by X-ray diffraction at 2.5 Å resolution. Released 9 May 2018.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Danio rerio, Eptatretus burgeri, Petromyzon marinus
Chains: 4
Atoms: 9,515
Mol. weight: 142.06 kDa
Ligands: NAG
Released: 9 May 2018

Explore 6BXC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BXC contains 35 α-helices and 86 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: 11 helices, 31 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
α-helix	81	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
α-helix	192-194	3
β-strand	198-203	6	1
α-helix	219-222	4
β-strand	230-235	6	1
α-helix	243-252	10
β-strand	258-262	5	1
α-helix	287-289	3
β-strand	296-298	3	1
β-strand	306-307	2	4
β-strand	320-322	3	1
β-strand	330-331	2	4
β-strand	344-346	3	1
β-strand	355	1	5
α-helix	357-360	4
β-strand	368-370	3	1
β-strand	379	1	5
β-strand	392-394	3	1
β-strand	416-418	3	1
β-strand	424	1	6
α-helix	432-440	9
β-strand	445-446	2	1
β-strand	450	1	7
β-strand	451	1	6
β-strand	457	1	7
α-helix	458-460	3

Chain B: 11 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	8
β-strand	31-33	3	8
α-helix	42-44	3
β-strand	51-53	3	8
β-strand	61-62	2	9
β-strand	75-77	3	8
α-helix	81	1
β-strand	86-87	2	9
β-strand	100-102	3	8
β-strand	110-111	2	9
β-strand	124-126	3	8
α-helix	135-138	4
β-strand	150-152	3	8
α-helix	165-169	5
β-strand	175-177	3	8
α-helix	192-194	3
β-strand	198-203	6	8
α-helix	219-222	4
β-strand	230-235	6	8
α-helix	243-252	10
β-strand	258-262	5	8
α-helix	287-289	3
β-strand	296-298	3	8
β-strand	306-307	2	10
β-strand	320-322	3	8
β-strand	330-331	2	10
β-strand	344-346	3	8
β-strand	354-355	2	11
α-helix	357-360	4
β-strand	368-370	3	8
β-strand	378-379	2	11
β-strand	392-394	3	8
β-strand	416-418	3	8
β-strand	424	1	12
α-helix	432-440	9
β-strand	445-446	2	8
β-strand	451	1	12
α-helix	458-460	3

Chain C: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	18
β-strand	22-23	2	18
β-strand	27-29	3	19
β-strand	32-34	3	19
α-helix	43-44	2
β-strand	53-55	3	19
β-strand	77-79	3	19
β-strand	101-103	3	19
β-strand	125-127	3	19
β-strand	133	1	20
α-helix	141-149	9
α-helix	151-153	3
β-strand	154	1	19
β-strand	159	1	21
β-strand	160	1	20
β-strand	166	1	21
α-helix	167-169	3
α-helix	172-174	3
α-helix	177-179	3

Chain D: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	13
β-strand	22-23	2	13
β-strand	27-29	3	14
β-strand	32-34	3	14
α-helix	43-44	2
β-strand	53-55	3	14
β-strand	77-79	3	14
β-strand	101-103	3	14
β-strand	125-127	3	14
β-strand	133	1	15
β-strand	137	1	16
α-helix	138-140	3
α-helix	141-149	9
α-helix	151-153	3
β-strand	154	1	14
β-strand	159	1	17
β-strand	160	1	15
β-strand	166	1	17
α-helix	167-169	3
α-helix	172-174	3
β-strand	176	1	16
α-helix	177-179	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toll-like receptor 5b, Variable lymphocyte receptor B chimera	A, B	protein	455	Danio rerio, Eptatretus burgeri	F8W3J5 (AlphaFold model), Q4G1L2 (AlphaFold model)
Variable Lymphocyte Receptor 9 (VLR9)	C, D	protein	178	Petromyzon marinus

Sequence of entity 1 (A, B), FASTA

>6BXC_1 Toll-like receptor 5b, Variable lymphocyte receptor B chimera (chains A, B)
ADPGTSECSVIGYNAICINRGLHQVPELPAHVNYVDLSLNSIAELNETSFSRLQDLQFLK
VEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVL
SGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGK
HFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAKRFFDAIAGTK
IQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTD
LEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSYNHIR
ALGDQSFLGLPNLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW
LNKNSQKEQGSAKCSGSGKPVRSIICPTSASLVPR

Sequence of entity 2 (C, D), FASTA

>6BXC_2 Variable Lymphocyte Receptor 9 (VLR9) (chains C, D)
GGHHHHHHGSENLYFQGACPSQCSCSGTTVDCSGKSLASVPGGIPTTTQVLYLYDNQITK
LEPGVFDRLVNLQQLWLEINQLTSLPAGVFDNLTQLSILNMHTNQLKSIPRGAFDNLKSL
THIWLLNNPWDCACSDILYLSGWLGQHAGKEQGQAVCSGTNTPVRAVTEASTSPSKCP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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

Primary citation

VLR Recognition of TLR5 Expands the Molecular Characterization of Protein Antigen Binding by Non-Ig-based Antibodies. Gunn, R.J., Herrin, B.R., Acharya, S. et al. J Mol Biol (2018) 430:1350-1367. DOI 10.1016/j.jmb.2018.03.016 · PubMed

Other PDB entries of the same protein (UniProt F8W3J5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BXA 2.3 Å, Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with…

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