7KP8: Asymmetric mTNF-alpha hTNFR1 complex

asymmetric mTNF-alpha hTNFR1 complex. Determined by X-ray diffraction at 3.15 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 3.15 Å
Organisms: Mus musculus, Homo sapiens
Chains: 5
Atoms: 4,940
Mol. weight: 81.53 kDa
Ligands: A7G
Released: 13 Jan 2021

Explore 7KP8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KP8 contains 17 α-helices and 69 β-strands across 5 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.

Chains A and B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
β-strand	28-29	2	1
β-strand	36-38	3	1
β-strand	42-44	3	2
β-strand	47-49	3	2
β-strand	54-67	14	1
β-strand	75-82	8	2
β-strand	89-97	9	2
β-strand	112-125	14	1
β-strand	130-135	6	2
α-helix	138-140	3
β-strand	141	1	1
β-strand	150-155	6	1

Chain C: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	5
β-strand	28-29	2	5
β-strand	36-38	3	5
β-strand	42-44	3	6
β-strand	47-49	3	6
β-strand	54-67	14	5
β-strand	75-82	8	6
β-strand	86	1	7
β-strand	90-97	8	6
β-strand	112-125	14	5
β-strand	130-135	6	6
α-helix	138-140	3
β-strand	141	1	5
β-strand	150-155	6	5

Chain E: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	19-21	3	8
β-strand	29-31	3	8
α-helix	32	1
β-strand	33	1	9
α-helix	34	1
β-strand	37-41	5	10
α-helix	49-50	2
β-strand	51-54	4	10
α-helix	55-56	2
β-strand	59-60	2	11
β-strand	65	1	9
α-helix	70	1
β-strand	71-72	2	11
α-helix	73-74	2
α-helix	78-80	3
β-strand	83-86	4	12
β-strand	89	1	13
β-strand	92	1	13
β-strand	95-97	3	12
β-strand	102-108	7	14
β-strand	111-116	6	14
α-helix	117-119	3
β-strand	123-125	3	15
β-strand	137-139	3	15

Chain F: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	19-21	3	16
β-strand	29-31	3	16
β-strand	33	1	7
β-strand	37-41	5	17
α-helix	49-50	2
β-strand	51-54	4	17
α-helix	55-56	2
β-strand	59-60	2	18
β-strand	65	1	7
α-helix	70	1
β-strand	71-72	2	18
α-helix	73-74	2
α-helix	78-80	3
β-strand	83-86	4	19
β-strand	89	1	20
β-strand	92	1	20
β-strand	95-97	3	19
β-strand	102-108	7	21
β-strand	111-116	6	21
α-helix	117-119	3
β-strand	124-125	2	22
β-strand	137-138	2	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C	protein	147	Mus musculus	P06804 (AlphaFold model)
Tumor necrosis factor receptor superfamily member 1A	E, F	protein	142	Homo sapiens	P19438 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>7KP8_1 Tumor necrosis factor (chains A, B, C)
DKPVAHVVANHQVEEQLEWLSQRANALLANGMDLKDNQLVVPADGLYLVYSQVLFKGQGC
PDYVLLTHTVSRFAISYQEKVNLLSAVKSPCPKDTPEGAELKPWYEPIYLGGVFQLEKGD
QLSAEVNLPKYLDFAESGQVYFGVIAL

Sequence of entity 2 (E, F), FASTA

>7KP8_2 Tumor necrosis factor receptor superfamily member 1A (chains E, F)
VCPQGKYIHPQDNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCLSC
SKCRKEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLSCQEKQ
NTVCTCHAGFFLRENECVSSSN

Ligands and cofactors

ID	Name	Formula	Copies
A7G	1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-y…	C25 H25 F2 N5 O	1

Primary citation

Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF. McMillan, D., Martinez-Fleites, C., Porter, J. et al. Nat Commun (2021) 12:582-582. DOI 10.1038/s41467-020-20828-3 · PubMed

Other PDB entries of the same protein (UniProt P06804 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2TNF 1.4 Å, 1.4 a resolution structure of mouse tumor necrosis factor, towards modulation of its…
7KP7 2.65 Å, asymmetric mTNF-alpha hTNFR1 complex

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