3V47: N-terminal fragment of zebrafish TLR5

Crystal structure of the N-terminal fragment of zebrafish TLR5 in complex with Salmonella flagellin. Determined by X-ray diffraction at 2.47 Å resolution. Released 29 Feb 2012.

Method: X-ray diffraction
Resolution: 2.47 Å
Organisms: Danio rerio, Eptatretus burgeri, Salmonella enterica subsp. enterica serovar Dublin
Chains: 4
Atoms: 11,462
Mol. weight: 193.8 kDa
Ligands: NAG
Released: 29 Feb 2012

Explore 3V47 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V47 contains 49 α-helices and 103 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: 12 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
α-helix	197	1
β-strand	198-203	6	1
β-strand	208	1	4
α-helix	219-222	4
β-strand	230-235	6	1
α-helix	243-252	10
β-strand	258-262	5	1
α-helix	279-281	3
α-helix	287-289	3
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	354-355	2	6
α-helix	357-360	4
β-strand	368-370	3	1
β-strand	378-379	2	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	445-446	2	1
β-strand	450	1	8
β-strand	451	1	7
β-strand	457	1	8
α-helix	458-460	3

Chain B: 12 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	9
β-strand	31-33	3	9
α-helix	42-44	3
β-strand	51-53	3	9
β-strand	61-62	2	10
β-strand	75-77	3	9
α-helix	81	1
β-strand	86-87	2	10
β-strand	100-102	3	9
β-strand	110-111	2	10
β-strand	124-126	3	9
α-helix	135-138	4
β-strand	150-152	3	9
α-helix	165-169	5
β-strand	175-177	3	9
β-strand	183	1	11
α-helix	192-194	3
β-strand	198-203	6	9
β-strand	208	1	11
α-helix	219-222	4
β-strand	230-235	6	9
α-helix	243-252	10
β-strand	258-262	5	9
α-helix	279-281	3
α-helix	287-289	3
β-strand	296-298	3	9
β-strand	306-307	2	12
β-strand	320-322	3	9
β-strand	330-331	2	12
β-strand	344-346	3	9
β-strand	354-355	2	13
α-helix	357-360	4
β-strand	368-370	3	9
β-strand	378-379	2	13
β-strand	392-394	3	9
β-strand	416-418	3	9
β-strand	424	1	14
α-helix	432-440	9
β-strand	445-446	2	9
β-strand	450	1	15
β-strand	451	1	14
β-strand	457	1	15
α-helix	458-460	3

Chain C: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	65-100	36
α-helix	105-128	24
β-strand	130-131	2	16
β-strand	134-135	2	16
β-strand	141-146	6	17
β-strand	154-159	6	17
α-helix	177	1
β-strand	178-179	2	18
α-helix	180	1
α-helix	182-188	7
β-strand	193-200	8	19
β-strand	203-208	6	19
β-strand	214-216	3	19
α-helix	221-222	2
β-strand	223	1	19
β-strand	225-226	2	20
β-strand	233-234	2	20
β-strand	238-239	2	21
β-strand	345-346	2	21
α-helix	347	1
β-strand	348-349	2	20
α-helix	350	1
α-helix	352-357	6
β-strand	361-362	2	19
β-strand	365-368	4	19
β-strand	373-376	4	19
α-helix	377	1
β-strand	383-384	2	19
β-strand	389	1	19
β-strand	390-394	5	18
β-strand	400-404	5	18
α-helix	405-408	4
α-helix	412-414	3
α-helix	417-450	34
α-helix	452-455	4

Chain D: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	63-100	38
α-helix	105-128	24
β-strand	131	1	22
β-strand	134	1	22
β-strand	141-146	6	23
β-strand	154-159	6	23
β-strand	178-179	2	24
α-helix	182-188	7
β-strand	193-200	8	25
β-strand	203-208	6	25
β-strand	214-216	3	25
β-strand	223	1	25
β-strand	225	1	26
β-strand	234	1	26
α-helix	348	1
β-strand	349	1	26
α-helix	350	1
α-helix	352-357	6
β-strand	365-369	5	25
β-strand	372-376	5	25
β-strand	383-385	3	25
β-strand	388-389	2	25
β-strand	390-394	5	24
β-strand	400-404	5	24
α-helix	405-408	4
α-helix	413-414	2
α-helix	417-450	34
α-helix	452-455	4
α-helix	456-459	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toll-like receptor 5b and variable lymphocyte receptor B.61 chimeric protein	A, B	protein	455	Danio rerio, Eptatretus burgeri	B3DIN1 (AlphaFold model), Q4G1L2 (AlphaFold model)
Flagellin	C, D	protein	425	Salmonella enterica subsp. enterica serovar Dublin	Q06971 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3V47_1 Toll-like receptor 5b and variable lymphocyte receptor B.61 chimeric protein (chains A, B)
ADPGTSECSVIGYNAICINRGLHQVPELPAHVNYVDLSLNSIAELNETSFSRLQDLQFLK
VEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVL
SGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGK
HFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAKRFFDAIAGTK
IQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTD
LEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSYNHIR
ALGDQSFLGLPNLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW
LNKNSQKEQGSAKCSGSGKPVRSIICPTSASLVPR

Sequence of entity 2 (C, D), FASTA

>3V47_2 Flagellin (chains C, D)
GSAKDPQAIANRFTSNIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELSVQATN
GTNSDSDLKSIQDEIQQRLEEIDRVSNQTQFNGVKVLSQDNQMKIQVGANDGETITIDLQ
KIDVKSLGLDGFNVNGPKEATVGDLKSSFKNVTGYDTYAAGADKYRVDINSGAVVTDAVA
PDKVYVNAANGQLTTDDAENNTAVDLFKTTKSTAGTAEAKAIAGAIKGGKEGDTFDYKGV
TFTIDTKTGDDGNGKVSTTINGEKVTLTVADIAIGAADVNAATLQSSKNVYTSVVNGQFT
FDDKTKNESAKLSDLEANNAVKGESKITVNGAEYTANATGDKITLAGKTMFIDKTASGVS
TLINEDAAAAKKSTANPLASIDSALSKVDAVRSSLGAIQNRFDSAITNLGNTVTNLNSAR
SRIED

Ligands and cofactors

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

Primary citation

Structural basis of TLR5-flagellin recognition and signaling. Yoon, S.I., Kurnasov, O., Natarajan, V. et al. Science (2012) 335:859-864. DOI 10.1126/science.1215584 · PubMed

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

5GY2 2.1 Å, Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish…
3V44 2.83 Å, Crystal structure of the N-terminal fragment of zebrafish TLR5

Browse structure collections

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