8ACI: ARG-117 Fab

Structure of ARG-117 Fab in complex with a fragment of complement C2, neutral pH. Determined by X-ray diffraction at 1.85 Å resolution. Released 17 Jan 2024.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Homo sapiens, Lama glama
Chains: 4
Atoms: 5,649
Mol. weight: 83.16 kDa
Ligands: CA
Released: 17 Jan 2024

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

Secondary structure: helices and β-sheets

8ACI contains 25 α-helices and 75 β-strands across 4 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	55-57	3	1
β-strand	84-86	3	1
α-helix	87	1
β-strand	88-90	3	2
α-helix	91-92	2
β-strand	98-101	4	3
β-strand	106-108	3	2
β-strand	112-117	6	3
β-strand	122-124	3	4
β-strand	128-130	3	3
β-strand	131	1	5
β-strand	137	1	5
β-strand	143-145	3	4
β-strand	160-163	4	6
β-strand	172-177	6	6
α-helix	181	1
β-strand	182-184	3	7
β-strand	188-190	3	6
β-strand	191	1	8
β-strand	197	1	8
β-strand	203-205	3	7

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-52	8	10
β-strand	57-60	4	10
α-helix	62-64	3
β-strand	68-73	6	9
α-helix	74-76	3
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	105-108	4	10
β-strand	112-116	5	10
β-strand	122	1	11
α-helix	123-124	2
β-strand	125-129	5	12
α-helix	133-135	3
β-strand	136-137	2	12
β-strand	140-150	11	12
β-strand	151	1	11
β-strand	156-159	4	13
α-helix	160-162	3
β-strand	164	1	13
β-strand	168-170	3	12
α-helix	171-173	3
β-strand	174-175	2	12
β-strand	181-190	10	12
α-helix	191-193	3
β-strand	199-205	7	13
α-helix	206-208	3
β-strand	210-216	7	13

Chain K: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	14
β-strand	12-14	3	15
β-strand	20-27	8	14
α-helix	31-33	3
β-strand	36-41	6	15
β-strand	48-53	6	15
β-strand	60-62	3	15
β-strand	70-75	6	14
β-strand	80-85	6	14
α-helix	90-92	3
β-strand	94-101	8	15
β-strand	110-113	4	15
β-strand	117-121	5	15

Chain L: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	16
β-strand	10-13	4	10
β-strand	19-25	7	16
β-strand	30-31	2	17
β-strand	34-35	2	17
β-strand	37-42	6	10
β-strand	49-53	5	10
β-strand	57-58	2	10
α-helix	59	1
β-strand	66-71	6	16
β-strand	74-79	6	16
α-helix	84-86	3
β-strand	88-94	7	10
α-helix	100	1
β-strand	101-102	2	10
β-strand	106-110	5	10
β-strand	115	1	18
α-helix	116-117	2
β-strand	118-122	5	19
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	19
β-strand	144	1	18
β-strand	148-154	7	20
β-strand	157-158	2	20
α-helix	159	1
β-strand	163-167	5	19
α-helix	168-171	4
β-strand	177-186	10	19
α-helix	187-192	6
β-strand	195-202	8	20
β-strand	209-214	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C2b fragment	A	protein	197	Homo sapiens	P06681 (AlphaFold model)
ARGX-117 Fab heavy chain	H	protein	219	Homo sapiens
nanobody specific for kappa light chain of Fab	K	protein	128	Lama glama
ARGX-117 Fab light chain	L	protein	218	Homo sapiens

Sequence of entity 1 (A), FASTA

>8ACI_1 Complement C2b fragment (chains A)
APSCPQNVNISGGTFTLSHGWAPGSLLTYSCPQGLYPSPASRLCKSSGQWQTPGATRSLS
KAVCKPVRCPAPVSFENGIYTPRLGSYPVGGNVSFECEDGFILRGSPVRQCRPNGMWDGE
TAVCDNGAGHCPNPGISLGAVRTGFRFGHGDKVRYRCSSNLVLTGSSERECQGNGVWSGT
EPICRQPYSYDFPEDVA

Sequence of entity 2 (H), FASTA

>8ACI_2 ARGX-117 Fab heavy chain (chains H)
EVQLVQSGAEVKKPGASVKVSCKASGYTFTDYNMDWVRQATGQGLEWIGDINPNYESTGY
NQKFKGRATMTVDKSISTAYMELSSLRSEDTAVYYCAREDDHDAFAYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 3 (K), FASTA

>8ACI_3 nanobody specific for kappa light chain of Fab (chains K)
QVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFY
ADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVS
SEHHHHHH

Sequence of entity 4 (L), FASTA

>8ACI_4 ARGX-117 Fab light chain (chains L)
DNVLTQSPDSLAVSLGERATISCRASKSVRTSGYNYMHWYQQKPGQPPKLLIYLASNLKS
GVPDRFSGSGSGTDFTLTISSLQAEDAATYYCQHSRELPYTFGQGTKLEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Water and common crystallization additives (CL, MPD) are not listed.

Primary citation

Structure-function analysis of ARGX-117, a calcium- and pH-dependent clinical phase complement C2 blocking antibody. Olesen, H.G., Andersen, G.R. To be published.

Other PDB entries of the same protein (UniProt P06681 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ERB 1.8 Å, The Crystal Structure of C2b, a Fragment of Complement Component C2 produced during…
8ACF 1.8 Å, Structure of the argX-117 in complex with a complement C2 fragment at low pH
2I6Q 2.1 Å, Complement component C2a
9ZCJ 2.6 Å, Therapeutic antibody with captured antigen
2I6S 2.7 Å, Complement component C2a
9U60 2.9 Å, C3 convertases zymogen C4b2 in loading state
9U5Z 3.1 Å, C3 convertases zymogen C4b2 in activation state
9U61 3.1 Å, CP/MBL pathways C3 convertase C4b2a and C3 complex
9QJ5 3.5 Å, Structure of the Complement classical and lectin pathway proconvertase, C4b2
9QK2 3.5 Å, Structure of the Complement classical and lectin pathway C3 convertase in complex with…
9QJ4 3.9 Å, Structure of the Complement classical and lectin pathway proconvertase, C4b2
9QPY 4.3 Å, Structure of the Complement classical and lectin pathway C3 convertase

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