5ZLN: Mouse TLR9

Crystal structure of mouse TLR9 in complex with two DNAs (CpG DNA and TCGCCA DNA). Determined by X-ray diffraction at 2.3 Å resolution. Released 25 Apr 2018.

Method
X-ray diffraction
Resolution
2.3 Å
Organisms
Mus musculus, synthetic construct
Chains
6
Atoms
13,446
Mol. weight
193.5 kDa
Ligands
NAG
Released
25 Apr 2018

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

Secondary structure: helices and β-sheets

5ZLN contains 55 α-helices and 102 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: 27 helices, 51 β-strands

ElementResiduesLengthSheet
β-strand36-3721
β-strand42-4431
β-strand67-6931
β-strand77-7822
α-helix84-863
β-strand91-9331
β-strand9813
α-helix101-1033
β-strand113-11422
β-strand127-12931
β-strand13313
α-helix138-1403
β-strand147-14931
β-strand157-15824
β-strand171-17331
β-strand17915
β-strand18215
β-strand189-19024
β-strand203-20531
α-helix214-2152
β-strand224-22631
β-strand234-23526
α-helix237-2404
β-strand248-25031
α-helix258-2603
α-helix266-2683
β-strand274-27526
β-strand288-29031
α-helix301-3044
β-strand312-31431
α-helix323-3264
β-strand338-34031
α-helix345-3462
β-strand35117
α-helix358-3625
β-strand368-37031
β-strand37617
β-strand378-37928
α-helix385-3873
β-strand395-39731
β-strand405-40628
α-helix408-4125
β-strand419-42131
α-helix467-4715
β-strand477-47931
α-helix490-4934
β-strand501-50331
β-strand526-52831
β-strand550-55231
α-helix558-5614
α-helix570-5745
β-strand580-58231
β-strand597-59829
β-strand603-60531
α-helix611-6144
β-strand627-62829
β-strand633-63531
α-helix646-6505
β-strand658-66031
α-helix671-6766
β-strand682-68431
β-strand693110
α-helix6991
β-strand706-70831
β-strand717110
β-strand730-73231
α-helix743-7453
α-helix747-7526
β-strand755-75731
β-strand763-764211
α-helix771-7777
α-helix779-7813
α-helix785-7884
β-strand790112
β-strand791-793311
α-helix795-7973
β-strand798111
β-strand801112
Chain B: 28 helices, 51 β-strands
ElementResiduesLengthSheet
β-strand36-37213
α-helix39-413
β-strand42-44313
β-strand67-69313
β-strand77-78214
α-helix84-863
β-strand91-93313
β-strand98115
α-helix101-1033
β-strand113-114214
β-strand127-129313
β-strand133115
α-helix138-1403
β-strand147-149313
β-strand157-158216
β-strand171-173313
β-strand179117
β-strand182117
β-strand189-190216
β-strand203-205313
α-helix214-2152
β-strand224-226313
β-strand234-235218
α-helix237-2404
β-strand248-250313
α-helix258-2603
α-helix266-2683
β-strand274-275218
β-strand288-290313
α-helix301-3044
β-strand312-314313
α-helix323-3264
β-strand338-340313
α-helix345-3462
β-strand351119
α-helix358-3625
β-strand368-370313
β-strand376119
β-strand378-379220
α-helix385-3873
β-strand395-397313
β-strand405-406220
α-helix408-4125
β-strand419-421313
α-helix467-4715
β-strand477-479313
α-helix490-4934
β-strand501-503313
β-strand526-528313
β-strand550-552313
α-helix558-5614
α-helix570-5745
β-strand580-582313
β-strand597-598221
β-strand603-605313
α-helix611-6144
β-strand627-628221
β-strand633-635313
α-helix646-6505
β-strand658-660313
α-helix671-6766
β-strand682-684313
β-strand693122
α-helix698-6992
β-strand706-708313
β-strand717122
β-strand730-732313
α-helix743-7453
α-helix747-7526
β-strand755-757313
β-strand763-764223
α-helix771-7777
α-helix779-7813
α-helix785-7884
β-strand790124
β-strand791-793323
α-helix795-7973
β-strand798123
β-strand801124

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Toll-like receptor 9A, Bprotein793Mus musculusQ9EQU3 (AlphaFold model)
DNA (5'-d(*ap*gp*gp*cp*gp*tp*tp*tp*tp*t)-3')C, DDNA10synthetic construct
DNA (5'-d(*tp*cp*gp*c)-3')E, FDNA6synthetic construct
Sequence of entity 1 (A, B), FASTA
>5ZLN_1 Toll-like receptor 9 (chains A, B)
LGTLPAFLPCELKPHGLVDCNWLFLKSVPRFSAAASCSNITRLSLISNRIHHLHNSDFVH
LSNLRQLNLKWNCPPTGLSPLHFSCHMTIEPRTFLAMRTLEELNLSYNGITTVPRLPSSL
VNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSNLTHLS
LKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLANLTSLRVLDVGGNCRRCDHAPNPC
IECGQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVNMSVLDLSENFLYESIQ
HTNAFQNLTRLRKLNLSFNYRKKVSFARLHLASSFKNLVSLQELNMNGIFFRSLNKYTLR
WLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTLSEATPEEADDAE
QEELLSADPHPAPLSTPASKNFMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLS
HNSIAQAVQGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQPFSMKGI
GHNFSFVAHLSMLHSLSLAHNDIHTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFF
QGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFQWTSLSFLPNLEVLDL
AGNQLKALTNGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSW
FGPIVMNLTVLDVRSNPLHCACGAAFVDLLLEVQTKVPGLANGVKCGSPGQLQGRSIFAQ
DLRLCLDEVLSWD
Sequence of entity 2 (C, D), FASTA
>5ZLN_2 DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3') (chains C, D)
AGGCGTTTTT
Sequence of entity 3 (E, F), FASTA
>5ZLN_3 DNA (5'-D(*TP*CP*GP*C)-3') (chains E, F)
TCGCCA

Ligands and cofactors

IDNameFormulaCopies
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O63

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

Primary citation

Structural basis for species-specific activation of mouse Toll-like receptor 9. Ishida, H., Ohto, U., Shibata, T. et al. FEBS Lett (2018) 592:2636-2646. DOI 10.1002/1873-3468.13176 · PubMed

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

Browse structure collections

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