8BLQ: CODV-IL13-RefAb triple complex

Cryo-EM structure of the CODV-IL13-RefAb triple complex. Determined by electron microscopy at 3.97 Å resolution. Released 7 Jun 2023.

Method: Electron microscopy
Resolution: 3.97 Å
Organism: Homo sapiens
Chains: 5
Atoms: 9,210
Mol. weight: 130.97 kDa
Released: 7 Jun 2023

Explore 8BLQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BLQ contains 32 α-helices and 126 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.

Chain A: 8 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	20	1	3
β-strand	22-25	4	1
α-helix	33	1
β-strand	34-38	5	2
β-strand	49-51	3	2
β-strand	58-60	3	2
β-strand	70	1	3
β-strand	73	1	4
β-strand	78	1	4
β-strand	81	1	3
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	100-102	3	5
β-strand	107-109	3	5
β-strand	117-121	5	2
β-strand	127-131	5	6
β-strand	135	1	7
β-strand	145-149	5	6
α-helix	153-155	3
β-strand	158-163	6	8
β-strand	170-175	6	8
β-strand	181-182	2	8
β-strand	191-192	2	9
β-strand	195-196	2	6
β-strand	201-202	2	6
β-strand	205-206	2	9
α-helix	211-213	3
β-strand	216-217	2	8
β-strand	220-222	3	8
β-strand	229-231	3	8
β-strand	236	1	8
β-strand	239	1	7
α-helix	252	1
β-strand	253-255	3	10
β-strand	267-268	2	11
β-strand	270-272	3	10
β-strand	276	1	12
β-strand	282-285	4	13
α-helix	286-288	3
β-strand	294-300	7	14
β-strand	310	1	12
β-strand	311-316	6	14
β-strand	317-318	2	11
α-helix	319	1
α-helix	322	1
β-strand	326	1	15
β-strand	327-330	4	13
β-strand	331	1	16
β-strand	336	1	16
β-strand	341	1	15

Chain B: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-12	3	18
β-strand	21-25	5	17
β-strand	30-31	2	19
β-strand	34-35	2	19
β-strand	37-40	4	20
β-strand	41-42	2	21
β-strand	50-53	4	20
β-strand	57-58	2	20
α-helix	59	1
β-strand	68-69	2	17
β-strand	74-77	4	17
α-helix	84-86	3
β-strand	89-90	2	21
β-strand	93-94	2	20
β-strand	101-102	2	20
β-strand	106	1	21
β-strand	107-109	3	18
β-strand	128	1	22
β-strand	137	1	23
β-strand	140-142	3	23
β-strand	152-156	5	24
β-strand	162-167	6	24
β-strand	171-172	2	24
β-strand	180-183	4	23
β-strand	188-193	6	23
α-helix	198-200	3
β-strand	203-207	5	24
β-strand	216	1	24
β-strand	220	1	24
β-strand	221	1	22
β-strand	238-240	3	25
α-helix	242-244	3
α-helix	245-248	4
β-strand	252-262	11	25
β-strand	267-269	3	26
β-strand	272-273	2	27
β-strand	277	1	27
β-strand	285-286	2	25
α-helix	287-290	4
β-strand	296-305	10	25
α-helix	306-310	5
β-strand	315-317	3	27
β-strand	319-321	3	26
β-strand	330-332	3	27

Chain C: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	28
β-strand	18-22	5	29
β-strand	33-37	5	28
β-strand	44-45	2	28
β-strand	48	1	30
β-strand	52	1	30
β-strand	61-66	6	29
β-strand	69-74	6	29
α-helix	79-81	3
β-strand	84-88	5	28
β-strand	89-90	2	31
β-strand	97-98	2	31
β-strand	103-107	5	28
β-strand	113	1	32
β-strand	116-120	5	33
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	33
β-strand	142	1	32
β-strand	148-150	3	34
β-strand	151-152	2	35
β-strand	155-156	2	35
β-strand	161-163	3	33
β-strand	167	1	33
β-strand	174-182	9	33
α-helix	184-189	6
β-strand	193-199	7	34
β-strand	202-208	7	34

Chain D: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-38	14
α-helix	44	1
α-helix	46-49	4
β-strand	52-53	2	36
α-helix	62-69	8
α-helix	79-88	10
α-helix	95-97	3
α-helix	101-104	4
β-strand	107-108	2	36
α-helix	110-126	17

Chain E: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	37
β-strand	10-12	3	38
β-strand	18-25	8	37
α-helix	29-31	3
β-strand	33-39	7	38
β-strand	45-51	7	38
β-strand	58-60	3	38
β-strand	68-73	6	37
β-strand	78-83	6	37
β-strand	92-99	8	38
β-strand	112	1	38
β-strand	117-120	4	38
α-helix	126-128	3
β-strand	129-132	4	39
α-helix	138-140	3
β-strand	147-154	8	39
β-strand	159-163	5	40
α-helix	175-177	3
β-strand	178-179	2	39
β-strand	185-191	7	39
α-helix	195-197	3
β-strand	204-209	6	40
β-strand	214-219	6	40

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CODV-Fab, heavy chain	A	protein	343	Homo sapiens
CODV-Fab, light chain	B	protein	334	Homo sapiens
RefAb, light chain	C	protein	212	Homo sapiens
Interleukin-13, human	D	protein	109	Homo sapiens	P35225 (AlphaFold model)
RefAb, heavy chain	E	protein	222	Homo sapiens

Sequence of entity 1 (A), FASTA

>8BLQ_1 CODV-Fab, heavy chain (chains A)
VQLQQSGPELVKPGASVKISCKASGYSFTSYWIHWIKQRPGQGLEWIGMIDPSDGETRLN
QRFQGRATLTVDESTSTAYMQLRSPTSEDSAVYYCTRLKEYGNYDSFYFDVWGAGTLVTV
SSGEVQLKESGPGLVAPGGSLSITCTVSGFSLTDSSINWVRQPPGKGLEWLGMIWGDGRI
DYADALKSRLSISKDSSKSQVFLEMTSLRTDDTATYYCARDGYFPYAMDFWGQGTSVTVS
SGGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 2 (B), FASTA

>8BLQ_2 CODV-Fab, light chain (chains B)
DIVLTQSPASLAVSLGQRATISCRASESVDSYGQSYMHWYQQKAGQPPKLLIYLASNLES
GVPARFSGSGSRTDFTLTIDPVQAEDAATYYCQQNAEDSRTFGGGTKLEIKGGGGGGGDI
QMTQSPASLSVSVGDTITLTCHASQNIDVWLSWFQQKPGNIPKLLIYKASNLHTGVPSRF
SGSGSGTGFTLTISSLQPEDIATYYCQQAHSYPFTFGGGTKLEIKGGGGGRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 3 (C), FASTA

>8BLQ_3 RefAb, light chain (chains C)
YVLTQPPSVSVAPGKTARITCGGNIIGSKLVHWYQQKPGQAPVLVIYDDGDRPSGIPERF
SGSNSGNTATLTISRVEAGDEADYYCQVWDTGSDPVVFGGGTKLTVLGQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

Sequence of entity 4 (D), FASTA

>8BLQ_4 Interleukin-13, human (chains D)
PPSTALRELIEELVNITQNQKAPLCNGSMVWSINLTAGMYCAALESLINVSGCSAIEKTQ
RMLSGFCPHKVSAGQFSSLHVRDTKIEVAQFVKDLLLHLKKLFREGQFN

Sequence of entity 5 (E), FASTA

>8BLQ_5 RefAb, heavy chain (chains E)
VQLVQSGAEVKKPGASVKVSCKASGYTFTNYGLSWVRQAPGQGLEWMGWISANNGDTNYG
QEFQGRVTMTTDTSTSTAYMELRSLRSDDTAVYYCARDSSSSWARWFFDLWGRGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Primary citation

Structural insights into the bi-specific cross-over dual variable antibody architecture by cryo-EM. Fernandez-Martinez, D., Tully, M.D., Leonard, G. et al. Sci Rep (2023) 13:8694-8694. DOI 10.1038/s41598-023-35678-4 · PubMed

Other PDB entries of the same protein (UniProt P35225 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3L5X 1.9 Å, Crystal structure of the complex between IL-13 and H2L6 FAB
4I77 1.9 Å, Lebrikizumab Fab bound to IL-13
5L6Y 1.99 Å, il13 in complex with tralokinumab
3L5W 2.0 Å, Crystal structure of the complex between IL-13 and C836 FAB
4PS4 2.8 Å, Crystal structure of the complex between IL-13 and M1295 FAB
3BPO 3.0 Å, Crystal structure of the IL13-IL4R-IL13Ra ternary complex
5E4E 3.0 Å, Engineered Interleukin-13 bound to receptor
3LB6 3.05 Å, The structure of IL-13 in complex with IL-13Ralpha2
3G6D 3.2 Å, Crystal structure of the complex between CNTO607 Fab and IL-13
1GA3 NMR structure of interleukin-13
1IJZ Solution Structure of Human IL-13
1IK0 Solution Structure of Human IL-13

Browse structure collections

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