8HLB: Biparatopic antibody Bp109-92

Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2. Determined by electron microscopy at 3.63 Å resolution. Released 4 Oct 2023.

Method: Electron microscopy
Resolution: 3.63 Å
Organisms: Homo sapiens, Escherichia coli (strain K12)
Chains: 5
Atoms: 7,461
Mol. weight: 158.51 kDa
Released: 4 Oct 2023

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

Secondary structure: helices and β-sheets

8HLB contains 24 α-helices and 111 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: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	17-19	3
β-strand	22-24	3	1
β-strand	31-33	3	1
β-strand	35	1	2
β-strand	39-43	5	3
β-strand	52-55	4	3
β-strand	66	1	2
β-strand	84	1	4
β-strand	96	1	4
β-strand	102-104	3	5
β-strand	115-117	3	5

Chain B: 5 helices, 31 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	34-39	6	8
β-strand	46-51	6	8
β-strand	57-58	2	8
β-strand	67	1	6
β-strand	70-72	3	6
β-strand	77-82	6	6
β-strand	91	1	9
β-strand	92-94	3	8
β-strand	96	1	10
β-strand	107	1	10
β-strand	113	1	9
β-strand	114-115	2	7
α-helix	119-120	2
β-strand	121	1	11
α-helix	122-123	2
β-strand	124-128	5	12
β-strand	136	1	13
β-strand	139	1	13
β-strand	142	1	14
β-strand	143-149	7	12
β-strand	150	1	11
β-strand	155-158	4	15
α-helix	159-161	3
β-strand	169	1	16
α-helix	170-172	3
β-strand	173-174	2	12
β-strand	180-182	3	12
β-strand	184	1	16
β-strand	186	1	14
β-strand	189	1	13
α-helix	190-192	3
β-strand	198-204	7	15
β-strand	209-215	7	15

Chain C: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	11-12	2	18
β-strand	19-21	3	19
β-strand	22-25	4	17
β-strand	37-38	2	20
β-strand	41-42	2	21
α-helix	47-48	2
β-strand	49	1	21
β-strand	54	1	22
β-strand	57	1	22
α-helix	58-59	2
β-strand	68-71	4	19
β-strand	74-79	6	19
β-strand	89-90	2	21
β-strand	93-94	2	20
α-helix	100	1
β-strand	108-109	2	18
β-strand	120-122	3	23
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-139	7	23
β-strand	150-154	5	24
β-strand	157-158	2	24
β-strand	163-164	2	23
β-strand	167	1	25
α-helix	169-171	3
β-strand	179	1	25
β-strand	180-186	7	23
α-helix	187-190	4
β-strand	196-200	5	24
β-strand	213	1	24

Chain D: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	26
β-strand	11-12	2	27
β-strand	19-25	7	26
β-strand	35-39	5	28
β-strand	45	1	28
β-strand	48-50	3	28
β-strand	51-52	2	29
β-strand	57-58	2	29
β-strand	68-73	6	26
β-strand	78-83	6	26
α-helix	88-90	3
β-strand	92-98	7	28
β-strand	108-109	2	28
α-helix	110-112	3
β-strand	113-115	3	28
β-strand	116-117	2	27
β-strand	126-129	4	30
α-helix	137-139	3
β-strand	143-149	7	30
β-strand	151	1	31
β-strand	158-160	3	32
α-helix	161-163	3
β-strand	170	1	30
α-helix	173-174	2
β-strand	175-176	2	31
β-strand	182-183	2	31
β-strand	186-189	4	30
α-helix	192-195	4
β-strand	202-206	5	32
β-strand	211-213	3	32

Chain E: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	33
β-strand	12-13	2	34
β-strand	19	1	35
β-strand	22-24	3	33
β-strand	34-37	4	36
β-strand	45-49	5	36
β-strand	53-54	2	36
α-helix	55	1
β-strand	66-67	2	33
β-strand	70-72	3	33
β-strand	75	1	35
β-strand	85-86	2	37
β-strand	87-89	3	36
β-strand	102-103	2	37
β-strand	105-106	2	34
α-helix	113	1
β-strand	114-117	4	38
α-helix	122-127	6
β-strand	134-137	4	38
β-strand	144-150	7	39
β-strand	154	1	39
β-strand	161-163	3	38
β-strand	174-177	4	38
α-helix	186-188	3
β-strand	192-198	7	39
β-strand	205-209	5	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor receptor superfamily member 1B,Maltose/maltodextrin-binding periplasmic…	A	protein	550	Homo sapiens, Escherichia coli (strain K12)	P0AEX9 (AlphaFold model), P20333 (AlphaFold model)
TR109 heavy chain	B	protein	236	Homo sapiens
TR109 light chain	C	protein	218	Homo sapiens
TR92 heavy chain	D	protein	238	Homo sapiens
TR92 light chain	E	protein	214	Homo sapiens

Sequence of entity 1 (A), FASTA

>8HLB_1 Tumor necrosis factor receptor superfamily member 1B,Maltose/maltodextrin-binding periplasmic protein (chains A)
LPAQVAFTPYAPEPGSTCRLREYYDQTAQMCCSKCSPGQHAKVFCTKTSDTVCDSCEDST
YTQLWNWVPECLSCGSRCSSDQVETQACTREQNRICTCRPGWYCALSKQEGCRLCAPLRK
CRPGFGVARPGTETSDVVCKPCAPGTFSNTTSSTDICRPHQICNVVAIPGNASMDAVCKI
EEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFW
AHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLL
PNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVG
VDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNY
GVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAV
ALKSYEEELVKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALK
DAQGHHHHHH

Sequence of entity 2 (B), FASTA

>8HLB_2 TR109 heavy chain (chains B)
QVQLKESGPGLVAPSQSLSITCTVSGFSLTVYGVNWVRQPPGKGLEWLGMIWGDGSTAYN
SALKSRLTITKDNSKTQVFLKMNSLQTDDTARYYCARDGRRYALDYWGQGTSVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCFNTHTCPPCPAPELLG

Sequence of entity 3 (C), FASTA

>8HLB_3 TR109 light chain (chains C)
DIVLTQSPTSLAVSLGQRATISCRASESVDSYGDSFLHWYQQKPGQPPILLIYRASNLDS
GIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPYTFGGGTKLEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (D), FASTA

>8HLB_4 TR92 heavy chain (chains D)
KVQLQQSGAELVKPGASVKLSCKASGYTFTESIIHWVKQRSGQGLEWIGWFYPGSDNINY
NEKFKDKATLTADKSSSTVYMELTRLTSEDSAVYFCASHEGPYVYFDYWGQGTTLTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLG

Sequence of entity 5 (E), FASTA

>8HLB_5 TR92 light chain (chains E)
DIVMTQSHKFMSTSVGDRVSITCKASQDVSTAVAWYQQKPGQSPKLLIYWTSTRHTGVPD
RFTGSGSGTDYTLTISSVQAEDLALYYCQHHYSTPYTFGGGTKLEIQRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection. Akiba, H., Fujita, J., Ise, T. et al. Commun Biol (2023) 6:987-987. DOI 10.1038/s42003-023-05326-8 · PubMed

Other PDB entries of the same protein (UniProt P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

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