8JJV: Truncated form of nanobody

Structure of truncated form of nanobody in complex with alpha-synuclein peptide. Determined by X-ray diffraction at 1.23 Å resolution. Released 10 Jan 2024.

Method: X-ray diffraction
Resolution: 1.23 Å
Organisms: Camelus dromedarius, Homo sapiens
Chains: 2
Atoms: 1,105
Mol. weight: 15.58 kDa
Released: 10 Jan 2024

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

Secondary structure: helices and β-sheets

8JJV contains 3 α-helices and 13 β-strands across 2 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	1
β-strand	18-23	6	2
α-helix	26-31	6
β-strand	34-39	6	3
β-strand	46-51	6	3
β-strand	57-59	3	3
β-strand	67-71	5	2
β-strand	77-82	6	2
α-helix	87-89	3
β-strand	91-97	7	3
α-helix	102-106	5
β-strand	109	1	2
β-strand	111-113	3	3
β-strand	114-116	3	1

Chain B: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	3
β-strand	7-10	4	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nanobody	A	protein	130	Camelus dromedarius
Alpha-synuclein peptide	B	protein	14	Homo sapiens	P37840 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8JJV_1 Nanobody (chains A)
QVQLQESGGGSVQAGGSLRLSCTISDAIFSRYAVGWFRQAPGKECELVSTITPDSTTTHS
DFVKGRFTLSRDNAKNTVYLQMHSLKPDDTAVYYCASRWRSVSEGCGGQGTQVTVSSAAA
YPYDVPDYGS

Sequence of entity 2 (B), FASTA

>8JJV_2 Alpha-synuclein peptide (chains B)
KTKEGVVHGVATVA

Primary citation

Structural insights into the unique recognition module between alpha-synuclein peptide and nanobody. Islam, Z., Vaikath, N.N., Hmila, I. et al. Protein Sci (2024) 33:e4875-e4875. DOI 10.1002/pro.4875 · PubMed

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

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…
8OG0 1.71 Å, Crystal structure of MJF14-6-4-2 Fab fragment in complex with epitope peptide

Browse structure collections

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