7DC8: Switch Ab Fab and hIL6R

Crystal structure of Switch Ab Fab and hIL6R in complex with ATP. Determined by X-ray diffraction at 2.76 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 2.76 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,244
Mol. weight: 147.12 kDa
Ligands: ATP
Released: 13 Jan 2021

Explore 7DC8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DC8 contains 40 α-helices and 127 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.

Chain A: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	9-13	4	2
β-strand	18-25	8	1
α-helix	27C-31	5
β-strand	34-38	5	2
α-helix	43-44	2
β-strand	45-48	4	2
β-strand	49	1	3
β-strand	53	1	3
β-strand	62-67	6	1
β-strand	70-76	7	1
β-strand	84-91	8	2
β-strand	96-98	3	2
β-strand	102-106	5	2
β-strand	112	1	4
α-helix	113-114	2
β-strand	115-119	5	5
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	5
β-strand	141	1	4
β-strand	146-151	6	6
β-strand	154-155	2	6
β-strand	160-162	3	5
α-helix	163-165	3
β-strand	166-167	2	5
β-strand	173-181	9	5
α-helix	183-188	6
β-strand	192-197	6	6
β-strand	202-207	6	6

Chain B: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	46-51	6	9
β-strand	57-59	3	9
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	9
β-strand	100E-103	4	9
β-strand	107-109	3	9
β-strand	110-111	2	8
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	138-145	8	11
β-strand	146	1	10
β-strand	151-154	4	12
β-strand	159	1	12
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
α-helix	171	1
β-strand	176-182	7	11
β-strand	195-200	6	12
α-helix	201-203	3
β-strand	205-210	6	12

Chain C: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	120-122	3	13
β-strand	123	1	14
β-strand	130-134	5	13
β-strand	146-153	8	15
α-helix	154-155	2
β-strand	160-164	5	16
β-strand	165-167	3	17
β-strand	174-178	5	17
β-strand	187-193	7	16
β-strand	202	1	16
α-helix	203-205	3
β-strand	206-209	4	16
α-helix	211-213	3
β-strand	214	1	18
α-helix	216-219	4
β-strand	220-227	8	19
β-strand	230-239	10	19
β-strand	251-258	8	20
β-strand	267-269	3	20
α-helix	270	1
β-strand	276-279	4	19
β-strand	288-296	9	20
α-helix	303-309	7
β-strand	310-312	3	20

Chain D: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	21
β-strand	9-13	4	22
β-strand	18-25	8	21
α-helix	27C-30	4
β-strand	34-38	5	22
β-strand	45-48	4	22
β-strand	49	1	23
β-strand	53	1	23
β-strand	62-67	6	21
β-strand	70-76	7	21
α-helix	80-82	3
β-strand	84-91	8	22
β-strand	96-98	3	22
β-strand	102-106	5	22
β-strand	112	1	24
α-helix	113-114	2
β-strand	115-119	5	25
α-helix	120-122	3
α-helix	123-127	5
β-strand	133-140	8	25
β-strand	141	1	24
β-strand	146-151	6	26
β-strand	155	1	26
β-strand	160-162	3	25
α-helix	163-165	3
β-strand	166-167	2	25
β-strand	173-179	7	25
α-helix	183-188	6
β-strand	192-198	7	26
β-strand	201-207	7	26

Chain E: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	27
β-strand	11-12	2	28
β-strand	18-25	8	27
α-helix	29-31	3
β-strand	34-39	6	29
β-strand	45-51	7	29
β-strand	57-59	3	29
β-strand	67-72	6	27
β-strand	77-82	6	27
α-helix	84-86	3
β-strand	88-95	8	29
α-helix	96-97	2
β-strand	100E-103	4	29
β-strand	107-109	3	29
β-strand	110-111	2	28
β-strand	117	1	30
β-strand	120-124	5	31
β-strand	137-145	9	31
β-strand	146	1	30
α-helix	149	1
β-strand	151-154	4	32
α-helix	155-157	3
β-strand	159	1	32
β-strand	163-170	8	31
α-helix	171	1
β-strand	176-183	8	31
β-strand	195-200	6	32
α-helix	201-203	3
β-strand	205-210	6	32

Chain F: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	120-122	3	17
β-strand	123	1	18
α-helix	129	1
β-strand	130-133	4	17
β-strand	147-153	7	16
β-strand	158-164	7	15
β-strand	165-167	3	13
β-strand	174-178	5	13
β-strand	187-194	8	15
β-strand	202	1	15
α-helix	203-205	3
β-strand	206-209	4	15
α-helix	211-213	3
β-strand	214	1	14
α-helix	216-219	4
β-strand	220-226	7	33
β-strand	234-239	6	33
β-strand	251-259	9	34
β-strand	266-269	4	34
α-helix	270	1
β-strand	276-279	4	33
α-helix	282-283	2
β-strand	288-296	9	34
α-helix	303-309	7
β-strand	310-312	3	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Switch Ab Fab light chain	A, D	protein	216	Homo sapiens
Switch Ab Fab heavy chain	B, E	protein	230	Homo sapiens
Interleukin-6 receptor subunit alpha	C, F	protein	218	Homo sapiens	P08887 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>7DC8_1 Switch Ab Fab light chain (chains A, D)
QSALTQPPSASGSPGQTVTISCTGTSTDVGDYAYVSWYQQHPGKAPKLMIYYVSKKPDGV
PDRFSGSKSGNTASLTVSGLQAEDEADYFCSLRSPGPYPLFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (B, E), FASTA

>7DC8_2 Switch Ab Fab heavy chain (chains B, E)
EVQLVESGGDLVKPGGGLRLSCAASGFTFSSYTMNWVRQAPGKGLEWVSSISSQSYHIYY
ADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARYGKLYSLNWVFDYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (C, F), FASTA

>7DC8_3 Interleukin-6 receptor subunit alpha (chains C, F)
DVPPEEPQLSCFRKSPLSNVVCEWGPRSTPSLTTKAVLLVRKFQNSPAEDFQEPCQYSQE
SQKFSCQLAVPEGDSSFYIVSMSVASSVGSKFSKTQTFQGCGILQPDPPANITVTAVARN
PRWLSVTWQDPHSWNSSFYRLRFELRYRAERSKTFTTWMVKDLQHHCVIHDAWSGLRHVV
QLRAQEEFGQGEWSEWSPEAMGTPWTESRSDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

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

Primary citation

Exploitation of Elevated Extracellular ATP to Specifically Direct Antibody to Tumor Microenvironment. Mimoto, F., Tatsumi, K., Shimizu, S. et al. Cell Rep (2020) 33:108542-108542. DOI 10.1016/j.celrep.2020.108542 · PubMed

Other PDB entries of the same protein (UniProt P08887 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1N26 2.4 Å, Crystal Structure of the extra-cellular domains of Human Interleukin-6 Receptor alpha…
5FUC 2.7 Å, Biophysical and cellular characterisation of a junctional epitope antibody that locks…
8QY5 3.1 Å, Structure of interleukin 6.
8QY6 3.16 Å, Structure of interleukin 6 (gp130 P496L mutant).
8IOW 3.2 Å, Cryo-EM structure of the sarilumab Fab/IL-6R complex
8D82 3.22 Å, Cryo-EM structure of human IL-6 signaling complex in detergent: model containing full…
8J6F 3.3 Å, Cryo-EM structure of the Tocilizumab Fab/IL-6R complex
1P9M 3.65 Å, Crystal structure of the hexameric human IL-6/IL-6 alpha receptor/gp130 complex
2ARW The solution structure of the membrane proximal cytokine receptor domain of the human…

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