4QDH: C-terminal Domain of Mouse TLR9

Crystal Structure of the C-terminal Domain of Mouse TLR9. Determined by X-ray diffraction at 2.4 Å resolution. Released 11 Jun 2014.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Eptatretus burgeri, Mus musculus
Chains: 2
Atoms: 6,532
Mol. weight: 100.53 kDa
Ligands: NAG
Released: 11 Jun 2014

Explore 4QDH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4QDH contains 20 α-helices and 54 β-strands across 2 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, 27 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
β-strand	11-13	3	1
α-helix	22-23	2
β-strand	32-34	3	1
β-strand	56-58	3	1
α-helix	69-72	4
β-strand	80-82	3	1
β-strand	91	1	2
β-strand	105-107	3	1
β-strand	114	1	2
β-strand	129-131	3	1
α-helix	150-153	4
β-strand	159-161	3	1
β-strand	176-177	2	3
β-strand	182-184	3	1
α-helix	190-195	6
β-strand	206-207	2	3
β-strand	212-214	3	1
α-helix	225-229	5
β-strand	237-239	3	1
α-helix	250-255	6
β-strand	261-263	3	1
β-strand	272	1	4
α-helix	277-278	2
β-strand	285-287	3	1
β-strand	296	1	4
β-strand	309-311	3	1
α-helix	329-331	3
β-strand	334-336	3	1
β-strand	358-360	3	1
β-strand	366	1	5
α-helix	370-382	13
β-strand	387-388	2	1
β-strand	392	1	6
β-strand	393	1	5
β-strand	399	1	6
α-helix	400-402	3

Chain B: 10 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	7
β-strand	11-13	3	7
α-helix	22-23	2
β-strand	32-34	3	7
β-strand	56-58	3	7
α-helix	69-72	4
β-strand	80-82	3	7
β-strand	91	1	8
β-strand	105-107	3	7
β-strand	114	1	8
β-strand	129-131	3	7
α-helix	150-153	4
β-strand	159-161	3	7
β-strand	176-177	2	9
β-strand	182-184	3	7
α-helix	190-195	6
β-strand	206-207	2	9
β-strand	212-214	3	7
α-helix	225-229	5
β-strand	237-239	3	7
α-helix	250-255	6
β-strand	261-263	3	7
β-strand	271-272	2	10
α-helix	277-278	2
β-strand	285-287	3	7
β-strand	295-296	2	10
β-strand	309-311	3	7
β-strand	334-336	3	7
β-strand	358-360	3	7
β-strand	366	1	11
α-helix	370-382	13
α-helix	384-386	3
β-strand	387-388	2	7
β-strand	392	1	12
β-strand	393	1	11
β-strand	399	1	12
α-helix	400-402	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Variable lymphocyte receptor B, Toll-like receptor 9 chimera	A, B	protein	438	Eptatretus burgeri, Mus musculus	Q4G1L2 (AlphaFold model), Q9EQU3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4QDH_1 Variable lymphocyte receptor B, Toll-like receptor 9 chimera (chains A, B)
ADPGGKACPSRCSCSGTEIRCNSKGLTSVPTGIPSSATRLELESNKLQSLPHGVFDKLTQ
LTKLSLSRNNLVTIKPEMFVNLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKL
DLYHWKSFSELPQLQALDLSYNSQPFSMKGIGHNFSFVTHLSMLQSLSLAHNDIHTRVSS
HLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPK
SLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTNGTLPNGTLLQKLDVSSNSI
VSVVPAFFALAVELKEVNLSHNILKTVDRSWFGPIVMNLKELALDTNQLKSVPDGIFDRL
TSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPTASLVPR
GSWSHPQFEKGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

Water and common crystallization additives (SO4) are not listed.

Primary citation

Crystal structure of the C-terminal domain of mouse TLR9. Collins, B., Wilson, I.A. Proteins (2014) 82:2874-2878. DOI 10.1002/prot.24616 · PubMed

Other PDB entries of the same protein (UniProt Q4G1L2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2Z62 1.7 Å, Crystal structure of the TV3 hybrid of human TLR4 and hagfish VLRB.61
2Z66 1.9 Å, Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61
2Z63 2.0 Å, Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61
5GY2 2.1 Å, Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish…
7MLM 2.1 Å, Crystal structure of mouse TLR4/MD-2 in complex with sulfatides
4QXE 2.2 Å, Crystal structure of LGR4 fused with hagfish VLR
4QXF 2.25 Å, crystal structure of human LGR4 and Rspo1
6BXA 2.3 Å, Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with…
2O6R 2.3 Å, Structural diversity of the hagfish Variable Lymphocyte Receptors B61
4BV4 2.35 Å, Structure and allostery in Toll-Spatzle recognition
3UL7 2.37 Å, Crystal structure of the TV3 mutant F63W
3A7C 2.4 Å, Crystal structure of TLR2-PE-DTPA complex

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