9LFL: Linker-extended biparatopic antibody BA1-GP4

Cryo-EM structure of linker-extended biparatopic antibody BA1-GP4 in complex with TNFR2. Determined by electron microscopy at 3.73 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 3.73 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 7,710
Mol. weight: 109.92 kDa
Released: 13 Aug 2025

Explore 9LFL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9LFL contains 28 α-helices and 96 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	17-19	3
β-strand	22	1	1
β-strand	33	1	1
α-helix	34-36	3
α-helix	49-51	3
β-strand	84	1	2
β-strand	96	1	2
β-strand	102-103	2	3
β-strand	116-117	2	3
β-strand	126	1	4
β-strand	140	1	4

Chain B: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	5
β-strand	9-12	4	6
β-strand	14	1	7
β-strand	16	1	7
β-strand	19	1	8
β-strand	22-23	2	8
β-strand	24-25	2	5
β-strand	34-38	5	6
β-strand	46-51	6	6
β-strand	58-60	3	6
α-helix	62-64	3
β-strand	68-73	6	8
β-strand	78-83	6	8
β-strand	93-95	3	6
β-strand	113-117	5	6
β-strand	123	1	9
β-strand	126-130	5	10
α-helix	131-133	3
α-helix	134-136	3
β-strand	141-151	11	10
β-strand	152	1	9
β-strand	157-160	4	11
β-strand	165	1	11
β-strand	169-171	3	10
α-helix	172-174	3
β-strand	175-176	2	10
β-strand	182-191	10	10
α-helix	192-194	3
β-strand	200-206	7	11
α-helix	207-209	3
β-strand	211-217	7	11

Chain C: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	12
β-strand	11-13	3	13
β-strand	19-21	3	14
β-strand	23-24	2	12
β-strand	34-38	5	15
β-strand	45-49	5	15
β-strand	53-54	2	15
α-helix	55	1
β-strand	62-65	4	14
β-strand	72-75	4	14
α-helix	80-82	3
β-strand	85-87	3	15
β-strand	104-106	3	13
β-strand	111	1	16
α-helix	112-113	2
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	17
β-strand	140	1	16
β-strand	145-150	6	18
β-strand	153-154	2	18
β-strand	159-163	5	17
α-helix	164-167	4
β-strand	173-182	10	17
α-helix	183-187	5
β-strand	191-197	7	18
β-strand	205-210	6	18

Chain D: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	19
α-helix	12-13	2
β-strand	20-22	3	20
β-strand	23-25	3	19
β-strand	34-38	5	21
β-strand	46-52	7	21
β-strand	57-60	4	21
β-strand	71-73	3	20
β-strand	78-81	4	20
α-helix	88-90	3
β-strand	93-94	2	22
β-strand	95	1	21
β-strand	108-109	2	22
α-helix	118-120	3
β-strand	121-125	5	23
α-helix	126-128	3
α-helix	129-133	5
β-strand	136-146	11	23
β-strand	151-157	7	24
β-strand	160-162	3	24
β-strand	166-173	8	23
β-strand	179-189	11	23
α-helix	190-196	7
β-strand	199-205	7	24
β-strand	212-216	5	24

Chain E: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	25
β-strand	10-13	4	26
β-strand	23-24	2	25
β-strand	36-39	4	27
β-strand	46-47	2	27
β-strand	49	1	28
β-strand	55	1	28
α-helix	56	1
β-strand	63	1	29
β-strand	68	1	25
β-strand	71	1	25
β-strand	76	1	29
β-strand	86-89	4	27
β-strand	104-107	4	26
β-strand	114	1	30
β-strand	117-121	5	31
α-helix	126-130	5
β-strand	133-142	10	31
β-strand	143	1	30
β-strand	148-151	4	32
α-helix	152-154	3
β-strand	160-162	3	31
α-helix	163-165	3
β-strand	166-167	2	31
β-strand	173-181	9	31
α-helix	183-188	6
β-strand	191-197	7	32
β-strand	202-208	7	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor receptor superfamily member 1B	A	protein	152	Homo sapiens	P20333 (AlphaFold model)
TR92 heavy chain	B	protein	221	Mus musculus
TR92 light chain	C	protein	211	Mus musculus
TR96 heavy chain	D	protein	219	Mus musculus
TR96 light chain	E	protein	210	Mus musculus

Sequence of entity 1 (A), FASTA

>9LFL_1 Tumor necrosis factor receptor superfamily member 1B (chains A)
TPYAPEPGSTCRLREYYDQTAQMCCSKCSPGQHAKVFCTKTSDTVCDSCEDSTYTQLWNW
VPECLSCGSRCSSDQVETQACTREQNRICTCRPGWYCALSKQEGCRLCAPLRKCRPGFGV
ARPGTETSDVVCKPCAPGTFSNTTSSTDICRP

Sequence of entity 2 (B), FASTA

>9LFL_2 TR92 heavy chain (chains B)
KVQLQQSGAELVKPGASVKLSCKASGYTFTESIIHWVKQRSGQGLEWIGWFYPGSDNINY
NEKFKDKATLTADKSSSTVYMELTRLTSEDSAVYFCASHEGPYVYFDYWGQGTTLTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Sequence of entity 3 (C), FASTA

>9LFL_3 TR92 light chain (chains C)
IVMTQSHKFMSTSVGDRVSITCKASQDVSTAVAWYQQKPGQSPKLLIYWTSTRHTGVPDR
FTGSGSGTDYTLTISSVQAEDLALYYCQHHYSTPYTFGGGTKLEIQRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 4 (D), FASTA

>9LFL_4 TR96 heavy chain (chains D)
EVQLQQSGAELVKPGASVKLSCTPSGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGYTEY
DPKFQDKATITADTSSNTAYLQLSSLTSEDTAVYYCADTQLYYWGQGTTLTVSSASVAAP
SVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTY
SLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 5 (E), FASTA

>9LFL_5 TR96 light chain (chains E)
QIVLTQSPAIMSASLGERVTMTCTASSSVSSTYLHWYQQKPGSSPKLWIYSTSNLASGVP
ARFSGSGSGTSYSLTISNMEAEDAATYYCHQYHRSPLTFGAGTKLELKSSASTKGPSVFP
LAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVT
VPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Primary citation

Conversion of an agonistic anti-TNFR2 biparatopic antibody into an antagonist by insertion of peptide linkers into the hinge region. Otsuki, T., Matsumoto, S., Fujita, J. et al. J Biol Chem (2025) 301:110548-110548. DOI 10.1016/j.jbc.2025.110548 · PubMed

Other PDB entries of the same protein (UniProt P20333 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CU8 1.96 Å, Crystal Structure of TNFR2 TNFR2_mb1 Complex
1CA9 2.3 Å, Structure of tnf receptor associated factor 2 in complex with a peptide from tnf-R2
9LQI 2.95 Å, Structure of Nanobody-161 in complex of Tumor necrosis factor receptor 2 (TNFR2)
3ALQ 3.0 Å, Crystal structure of TNF-TNFR2 complex
8HLB 3.63 Å, Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2

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