8OG0: MJF14-6-4-2 Fab fragment

Crystal structure of MJF14-6-4-2 Fab fragment in complex with epitope peptide. Determined by X-ray diffraction at 1.71 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 1.71 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 3
Atoms: 3,447
Mol. weight: 46.86 kDa
Released: 27 Mar 2024

Explore 8OG0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OG0 contains 19 α-helices and 44 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 H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
β-strand	33-40	8	8
β-strand	46-53	8	8
β-strand	60-62	3	8
α-helix	64-66	3
β-strand	70-76	7	6
β-strand	79-84	6	6
α-helix	89-91	3
β-strand	93-101	9	8
α-helix	102	1
α-helix	106-109	4
β-strand	111-112	2	8
β-strand	116-118	3	8
β-strand	119-120	2	7
β-strand	126	1	9
α-helix	127-128	2
β-strand	129-133	5	10
β-strand	146-154	9	10
β-strand	155	1	9
β-strand	160-163	4	11
α-helix	164-166	3
β-strand	168	1	11
β-strand	172-174	3	10
α-helix	175-177	3
β-strand	178-179	2	10
β-strand	185-192	8	10
β-strand	202-207	6	11
α-helix	208-210	3
β-strand	212-217	6	11

Chain L: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	9-13	5	2
β-strand	18-24	7	1
α-helix	27-28	2
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	46-50	5	2
β-strand	54-55	2	2
α-helix	56	1
β-strand	63-68	6	1
β-strand	71-76	6	1
α-helix	81-83	3
β-strand	85-92	8	2
β-strand	101-103	3	2
β-strand	107-112	6	2
β-strand	116	1	3
α-helix	117-118	2
β-strand	119-123	5	4
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	4
β-strand	145	1	3
β-strand	149-154	6	5
β-strand	157-158	2	5
α-helix	159	1
β-strand	163-167	5	4
α-helix	168-171	4
β-strand	177-186	10	4
α-helix	187-190	4
β-strand	195-202	8	5
β-strand	205-212	8	5
α-helix	213-215	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab fragment light chain	L	protein	216	Oryctolagus cuniculus
Fab fragment heavy chain	H	protein	222	Oryctolagus cuniculus
Alpha-synuclein	P	protein	5	Homo sapiens	P37840 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>8OG0_1 Fab fragment light chain (chains L)
QVLTQTASSVSAAVGGTVTISCQSSQSVYKNNYLAWYQQKPGQPPNLLIYNASTLASGVS
SRFRGSGSGTQFTLTISGVQCDDAATYYCQGGFPCRTADCNVFGGGTEVVVKGDPVAPTV
LIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLS
STLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC

Sequence of entity 2 (H), FASTA

>8OG0_2 Fab fragment heavy chain (chains H)
QEQLVESGGDLVKPGASLTLTCTASGFSFSSNYWMCWFRQAPGKGPEWIACIYAGNSGST
YYATWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCWRRGAYGYYGDLNLWGPGTLVTV
SSGQPKAPSVFPLAPCCGDTPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQ
SSGLYSLSSVVSVTSSSQPEVTCNVAHPATNTKVDKTVAPST

Sequence of entity 3 (P), FASTA

>8OG0_3 Alpha-synuclein (chains P)
YEPEA

Primary citation

Structural basis of epitope recognition by anti-alpha-synuclein antibodies MJFR14-6-4-2. Lieknina, I., Reimer, L., Pantelejevs, T. et al. NPJ Parkinsons Dis (2024) 10:206-206. DOI 10.1038/s41531-024-00822-y · 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…

Browse structure collections

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