7KP7: Asymmetric mTNF-alpha hTNFR1 complex

asymmetric mTNF-alpha hTNFR1 complex. Determined by X-ray diffraction at 2.65 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 6,950
Mol. weight: 101.81 kDa
Ligands: NAG
Released: 13 Jan 2021

Explore 7KP7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KP7 contains 32 α-helices and 96 β-strands across 6 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, B and C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	14-19	6	3
β-strand	29-30	2	3
β-strand	37-39	3	3
β-strand	43-45	3	4
β-strand	48-50	3	4
β-strand	55-68	14	3
β-strand	76-84	9	4
β-strand	87-98	12	4
α-helix	104-106	3
β-strand	113-126	14	3
β-strand	131-136	6	4
α-helix	139-141	3
β-strand	142	1	3
β-strand	151-156	6	3

Chain D: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	19-21	3	17
β-strand	29-31	3	17
α-helix	32	1
β-strand	33	1	18
α-helix	34	1
β-strand	37-41	5	19
β-strand	51-54	4	19
α-helix	55-56	2
β-strand	59-60	2	20
β-strand	65	1	18
α-helix	70	1
β-strand	71-72	2	20
α-helix	73-74	2
α-helix	78-80	3
β-strand	83-86	4	21
β-strand	89	1	22
β-strand	92	1	22
β-strand	95-97	3	21
β-strand	102-106	5	23
β-strand	112-116	5	23
α-helix	117-118	2
β-strand	123-127	5	24
β-strand	130	1	25
β-strand	133	1	25
β-strand	136-139	4	24
β-strand	144-146	3	26
β-strand	149-151	3	26

Chain E: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	15-16	2
β-strand	19-21	3	7
β-strand	29-31	3	7
α-helix	32	1
β-strand	33	1	8
α-helix	34	1
β-strand	37-41	5	9
α-helix	48-50	3
β-strand	51-54	4	9
α-helix	55-56	2
β-strand	59-60	2	10
β-strand	65	1	8
α-helix	70	1
β-strand	71-72	2	10
α-helix	73-74	2
α-helix	78-80	3
β-strand	83-86	4	11
β-strand	89	1	12
β-strand	92	1	12
β-strand	95-97	3	11
β-strand	102-106	5	13
β-strand	112-116	5	13
α-helix	117-118	2
β-strand	123-127	5	14
β-strand	130	1	15
β-strand	133	1	15
α-helix	134-135	2
β-strand	136-139	4	14
β-strand	143-146	4	16
β-strand	149-152	4	16

Chain F: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	19-21	3	27
β-strand	29-31	3	27
α-helix	32	1
β-strand	33	1	28
α-helix	34	1
β-strand	37-41	5	29
α-helix	48-50	3
β-strand	51-54	4	29
α-helix	55-56	2
β-strand	59-60	2	30
β-strand	65	1	28
α-helix	70	1
β-strand	71-72	2	30
α-helix	73-74	2
α-helix	78-80	3
β-strand	83-86	4	31
β-strand	89	1	32
β-strand	92	1	32
β-strand	95-97	3	31
β-strand	102-106	5	33
β-strand	112-116	5	33
α-helix	117-118	2
β-strand	123-127	5	34
β-strand	130	1	35
β-strand	133	1	35
α-helix	134-135	2
β-strand	136-139	4	34
β-strand	143-146	4	36
β-strand	149-152	4	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C	protein	148	Mus musculus	P06804 (AlphaFold model)
Tumor necrosis factor receptor superfamily member 1A	D, E, F	protein	144	Homo sapiens	P19438 (AlphaFold model)

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

>7KP7_1 Tumor necrosis factor (chains A, B, C)
SDKPVAHVVANHQVEEQLEWLSQRANALLANGMDLKDNQLVVPADGLYLVYSQVLFKGQG
CPDYVLLTHTVSRFAISYQEKVNLLSAVKSPCPKDTPEGAELKPWYEPIYLGGVFQLEKG
DQLSAEVNLPKYLDFAESGQVYFGVIAL

Sequence of entity 2 (D, E, F), FASTA

>7KP7_2 Tumor necrosis factor receptor superfamily member 1A (chains D, E, F)
GSVCPQGKYIHPQDNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLRHCL
SCSKCRKEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLSCQE
KQNTVCTCHAGFFLRENECVSSSN

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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

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…
7KP8 3.15 Å, asymmetric mTNF-alpha hTNFR1 complex

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