3WPH: Mouse TLR9

Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 2). Determined by X-ray diffraction at 2.33 Å resolution. Released 11 Feb 2015.

Method: X-ray diffraction
Resolution: 2.33 Å
Organisms: Mus musculus, synthetic
Chains: 2
Atoms: 6,169
Mol. weight: 94.63 kDa
Ligands: NAG
Released: 11 Feb 2015

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

Secondary structure: helices and β-sheets

3WPH contains 22 α-helices and 53 β-strands across 1 chain. 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: 22 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	36-37	2	1
β-strand	42-44	3	1
β-strand	67-69	3	1
β-strand	77-78	2	2
α-helix	84-86	3
β-strand	91-93	3	1
β-strand	98	1	3
α-helix	99-101	3
β-strand	113-114	2	2
α-helix	119-121	3
β-strand	127-129	3	1
β-strand	133	1	3
α-helix	138-140	3
β-strand	147-149	3	1
β-strand	157-158	2	4
β-strand	171-173	3	1
β-strand	179	1	5
β-strand	182	1	5
β-strand	189-190	2	4
β-strand	203-205	3	1
α-helix	214-215	2
β-strand	224-226	3	1
β-strand	234-235	2	6
α-helix	237-240	4
β-strand	248-250	3	1
β-strand	256	1	7
β-strand	267	1	7
β-strand	274-275	2	6
β-strand	288-290	3	1
α-helix	301-304	4
β-strand	312-314	3	1
α-helix	321-326	6
β-strand	338-340	3	1
α-helix	358-362	5
β-strand	368-370	3	1
β-strand	378-379	2	8
α-helix	385-387	3
β-strand	395-397	3	1
β-strand	405-406	2	8
α-helix	408-412	5
β-strand	419-421	3	1
β-strand	477-479	3	1
α-helix	490-493	4
β-strand	501-503	3	1
β-strand	512	1	9
β-strand	526-528	3	1
β-strand	535	1	9
β-strand	550-552	3	1
α-helix	570-574	5
β-strand	580-582	3	1
β-strand	598	1	10
β-strand	603-605	3	1
α-helix	611-615	5
β-strand	628	1	10
β-strand	633-635	3	1
α-helix	646-650	5
β-strand	658-660	3	1
α-helix	671-676	6
β-strand	682-684	3	1
β-strand	693	1	11
α-helix	698-699	2
β-strand	706-708	3	1
β-strand	717	1	11
β-strand	730-732	3	1
α-helix	743-745	3
α-helix	747-751	5
β-strand	755-757	3	1
β-strand	763-764	2	12
α-helix	771-777	7
α-helix	779-781	3
α-helix	785-788	4
β-strand	790	1	13
β-strand	791-793	3	12
β-strand	798	1	12
β-strand	801	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toll-like receptor 9	A	protein	803	Mus musculus	Q9EQU3 (AlphaFold model)
DNA (5'-d(cpcptpgpgpaptpgpgpgpapa)-3')	B	DNA	12	synthetic

Sequence of entity 1 (A), FASTA

>3WPH_1 Toll-like receptor 9 (chains A)
RSPWLGTLPAFLPCELKPHGLVDCNWLFLKSVPRFSAAASCSNITRLSLISNRIHHLHNS
DFVHLSNLRQLNLKWNCPPTGLSPLHFSCHMTIEPRTFLAMRTLEELNLSYNGITTVPRL
PSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQL
THLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHA
PNPCIECGQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSENFLY
ESITHTNAFQNLTRLRKLNLSFNYRKKVSFARLHLASSFKNLVSLQELNMNGIFFRLLNK
YTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTLSEATPEEA
DDAEQEELLSADPHPAPLSTPASKNFMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQC
LSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQPFS
MKGIGHQFSFVTHLSMLQSLSLAHNDIHTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLY
LHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLE
VLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTV
DRSWFGPIVMQLTVLDVRSNPLHCACGAAFVDLLLEVQTKVPGLANGVKCGSPGQLQGRS
IFAQDLRLCLDEVLSWDEFLVPR

Sequence of entity 2 (B), FASTA

>3WPH_2 DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*GP*AP*A)-3') (chains B)
CCTGGATGGGAA

Ligands and cofactors

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

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

Primary citation

Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9. Ohto, U., Shibata, T., Tanji, H. et al. Nature (2015) 520:702-705. DOI 10.1038/nature14138 · PubMed

Other PDB entries of the same protein (UniProt Q9EQU3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3WPF 1.96 Å, Crystal structure of mouse TLR9 (unliganded form)
3WPG 2.25 Å, Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 1)
3WPI 2.25 Å, Crystal structure of mouse TLR9 in complex with inhibitory DNA_super
5ZLN 2.3 Å, Crystal structure of mouse TLR9 in complex with two DNAs (CpG DNA and TCGCCA DNA)
4QDH 2.4 Å, Crystal Structure of the C-terminal Domain of Mouse TLR9

Browse structure collections

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