3ONA: The SECRET domain

The SECRET domain in complex with CX3CL1. Determined by X-ray diffraction at 2.6 Å resolution. Released 17 Aug 2011.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Ectromelia virus, Homo sapiens
Chains: 2
Atoms: 1,772
Mol. weight: 26.98 kDa
Released: 17 Aug 2011

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

Secondary structure: helices and β-sheets

3ONA contains 7 α-helices and 15 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: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	165-173	9	1
β-strand	181-183	3	2
β-strand	188-191	4	2
β-strand	195-202	8	2
β-strand	208-216	9	1
β-strand	219-226	8	1
α-helix	231-233	3
β-strand	239-246	8	2
β-strand	252-254	3	2
β-strand	257	1	1
α-helix	258-259	2
β-strand	267-273	7	2
β-strand	279-287	9	1
β-strand	296-302	7	1
α-helix	315-317	3

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	15-16	2
α-helix	21-23	3
β-strand	24-29	6	3
α-helix	30-31	2
β-strand	39-43	5	3
β-strand	47-51	5	3
α-helix	56-69	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumour necrosis factor receptor	A	protein	163	Ectromelia virus	Q7TDW8
CX3CL1 protein	B	protein	80	Homo sapiens	P78423 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3ONA_1 Tumour necrosis factor receptor (chains A)
GAMGSFNSIDVEINMYPVNKTSCNSSIGSSSTISTSELTITLTHEDCTPVFIGDYYSVVD
KLATSGFFTNDKVHQDLTTQCKINLEIKCNSGRESRQLTPTTKVYLMPHSETVTVVGDCL
SNLDVYIVYANTDAIYSDMDVVAYHTSYILNVDHIPPNDCERD

Sequence of entity 2 (B), FASTA

>3ONA_2 CX3CL1 protein (chains B)
GAMGQHHGVTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQ
WVKDAMQHLDRQAAALTRNG

Primary citation

Structural basis of chemokine sequestration by CrmD, a poxvirus-encoded tumor necrosis factor receptor. Xue, X.G., Lu, Q.Y., Wei, H. et al. PLoS Pathog (2011) 7:e1002162-e1002162. DOI 10.1371/journal.ppat.1002162 · PubMed

Other PDB entries of the same protein (UniProt Q7TDW8), best resolution first:

3ON9 1.57 Å, The SECRET domain from Ectromelia virus

Browse structure collections

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