6CT7: Fab of anti-a-synuclein antibody BIIB054

Fab of anti-a-synuclein antibody BIIB054 in complex with acetylated a-synuclein peptide (1-10). Determined by X-ray diffraction at 1.9 Å resolution. Released 19 Dec 2018.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,019
Mol. weight: 95.02 kDa
Ligands: IPA
Released: 19 Dec 2018

Explore 6CT7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CT7 contains 33 α-helices and 91 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: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	21
β-strand	46-51	6	21
α-helix	54-56	3
β-strand	60-62	3	21
β-strand	70-75	6	19
α-helix	76-78	3
β-strand	80-85	6	19
α-helix	90-92	3
β-strand	94-100	7	21
β-strand	102-103	2	21
β-strand	107-109	3	21
β-strand	110-111	2	20
α-helix	115-116	2
β-strand	117	1	22
α-helix	118-119	2
β-strand	120-124	5	23
β-strand	135-145	11	23
β-strand	146	1	22
β-strand	151-154	4	24
α-helix	155-157	3
β-strand	163-165	3	23
α-helix	166-168	3
β-strand	169-170	2	23
β-strand	176-185	10	23
α-helix	187-190	4
β-strand	195-200	6	24
α-helix	201-203	3
β-strand	205-210	6	24

Chain B: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	13
β-strand	9-12	4	14
β-strand	18-23	6	13
β-strand	33-37	5	14
β-strand	44-47	4	14
β-strand	48	1	15
β-strand	52	1	15
α-helix	53-54	2
β-strand	61-66	6	13
β-strand	69-74	6	13
α-helix	79-81	3
β-strand	83-90	8	14
β-strand	97-99	3	14
β-strand	103-107	5	14
β-strand	113	1	16
α-helix	114-115	2
β-strand	116-120	5	17
α-helix	124-128	5
β-strand	132-141	10	17
β-strand	142	1	16
β-strand	147-152	6	18
β-strand	155-157	3	18
β-strand	161-163	3	17
α-helix	164-166	3
β-strand	167-168	2	17
β-strand	174-182	9	17
α-helix	184-189	6
β-strand	193-199	7	18
β-strand	202-208	7	18

Chain H: 10 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
α-helix	54-56	3
β-strand	60-62	3	9
β-strand	70-75	6	7
α-helix	76-78	3
β-strand	80-85	6	7
α-helix	90-92	3
β-strand	94-100	7	9
β-strand	102-103	2	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	115-116	2
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	131-132	2	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-185	10	11
α-helix	186-188	3
β-strand	194-200	7	12
α-helix	201-203	3
β-strand	205-211	7	12

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	9-12	4	2
β-strand	18-23	6	1
β-strand	33-37	5	2
β-strand	44-47	4	2
β-strand	48	1	3
β-strand	52	1	3
β-strand	61-66	6	1
β-strand	69-74	6	1
α-helix	79-81	3
β-strand	83-90	8	2
β-strand	97-99	3	2
β-strand	103-107	5	2
α-helix	110-112	3
β-strand	113	1	4
α-helix	114-115	2
β-strand	116-120	5	5
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	5
β-strand	142	1	4
β-strand	147-152	6	6
β-strand	155-157	3	6
β-strand	161-163	3	5
α-helix	164-166	3
β-strand	167-168	2	5
β-strand	174-182	9	5
α-helix	184-189	6
β-strand	193-199	7	6
β-strand	202-208	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BIIB054 Fab light chain	B, L	protein	214	Homo sapiens
BIIB054 Fab heavy chain	A, H	protein	220	Homo sapiens
Ace-met-asp-val-phe-met-lys-gly-leu-ser-lys	S, T	protein	11	Homo sapiens	P37840 (AlphaFold model)

Sequence of entity 1 (B, L), FASTA

>6CT7_1 BIIB054 Fab light chain (chains B, L)
SYELTQPPSVSVSPGQTARITCSGEALPMQFAHWYQQRPGKAPVIVVYKDSERPSGVPER
FSGSSSGTTATLTITGVQAEDEADYYCQSPDSTNTYEVFGGGTKLTVLSQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (A, H), FASTA

>6CT7_2 BIIB054 Fab heavy chain (chains A, H)
EVQLVESGGGLVEPGGSLRLSCAVSGFDFEKAWMSWVRQAPGQGLQWVARIKSTADGGTT
SYAAPVEGRFIISRDDSRNMLYLQMNSLKTEDTAVYYCTSAHWGQGTLVTVSSASTKGPS
VFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSS
VVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Sequence of entity 3 (S, T), FASTA

>6CT7_3 ACE-MET-ASP-VAL-PHE-MET-LYS-GLY-LEU-SER-LYS (chains S, T)
XMDVFMKGLSK

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	4

Primary citation

Development of an aggregate-selective, human-derived alpha-synuclein antibody BIIB054 that ameliorates disease phenotypes in Parkinson's disease models. Weihofen, A., Liu, Y., Arndt, J.W. et al. Neurobiol Dis (2018) 124:276-288. DOI 10.1016/j.nbd.2018.10.016 · PubMed

Other PDB entries of the same protein (UniProt P37840 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JJV 1.23 Å, Structure of truncated form of nanobody in complex with alpha-synuclein peptide
8JLY 1.29 Å, Structure of nanobody in complex with alpha-synuclein peptide
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
4R0U 1.38 Å, Tgvtava, an amyloid forming segment from alpha synuclein, residues 72-78
6I42 1.38 Å, Structure of the alpha-Synuclein PreNAC/Cyclophilin A-complex
4ZNN 1.41 Å, MicroED structure of the segment, GVVHGVTTVA, from the A53T familial mutant of…
4RIL 1.43 Å, Structure of the amyloid forming segment, GAVVTGVTAVA, from the NAC domain of…
4R0W 1.5 Å, Vvtgvta, an amyloid forming segment from alpha synuclein, residues 70-76
3Q26 1.54 Å, Cyrstal structure of human alpha-synuclein (10-42) fused to maltose binding protein (MBP)
3Q28 1.6 Å, Cyrstal structure of human alpha-synuclein (58-79) fused to maltose binding protein (MBP)
5CRW 1.6 Å, Crystal structure of the b'-a' domain of oxidized protein disulfide isomerase complexed…
2X6M 1.62 Å, Structure of a single domain camelid antibody fragment in complex with a C-terminal…

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