7TTX: Potent neutralizing antibody 10-40

Crystal structure of potent neutralizing antibody 10-40 in complex with Sarbecovirus bat RaTG13 receptor-binding domain. Determined by X-ray diffraction at 2.8 Å resolution. Released 27 Apr 2022.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Bat coronavirus RaTG13, Homo sapiens
Chains: 3
Atoms: 4,910
Mol. weight: 75.03 kDa
Ligands: NAG
Released: 27 Apr 2022

Explore 7TTX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TTX contains 22 α-helices and 66 β-strands across 3 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: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	335	1	1
β-strand	349	1	2
β-strand	354-357	4	2
β-strand	361	1	3
β-strand	362	1	1
α-helix	366-369	4
β-strand	376-380	5	2
α-helix	385-389	5
β-strand	392	1	3
β-strand	394-403	10	2
α-helix	405-407	3
α-helix	417-421	5
α-helix	424-426	3
β-strand	431-437	7	2
α-helix	439-442	4
β-strand	448	1	4
β-strand	452-454	3	5
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	6
β-strand	485	1	6
β-strand	488-489	2	6
β-strand	492-494	3	5
β-strand	497	1	4
β-strand	507-516	10	2
β-strand	524	1	3

Chain H: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11	1	8
β-strand	17-25	9	7
β-strand	35A-39	6	9
β-strand	46-51	6	9
β-strand	57-59	3	9
α-helix	64-66	3
β-strand	67-72	6	7
β-strand	77-82A	7	7
α-helix	84-86	3
β-strand	88-95	8	9
α-helix	96-98	3
β-strand	99-100	2	2
α-helix	100E	1
β-strand	100F-100G	2	2
β-strand	100L-103	4	9
β-strand	107-109	3	9
β-strand	110	1	8
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	150-154	5	12
β-strand	159	1	12
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	195-200	6	12
α-helix	201-203	3
β-strand	205-210	6	12

Chain L: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	13
β-strand	9-12	4	14
β-strand	17-24	8	13
α-helix	28-30	3
β-strand	34-38	5	14
β-strand	45-48	4	14
β-strand	49	1	15
β-strand	53	1	15
β-strand	62-66A	6	13
β-strand	70-76	7	13
β-strand	85-91	7	14
β-strand	96-98	3	14
β-strand	102-106	5	14
α-helix	109-111	3
β-strand	112	1	16
α-helix	113-114	2
β-strand	115-119	5	17
α-helix	123-126	4
β-strand	131-140	10	17
β-strand	141	1	16
β-strand	147-151	5	18
β-strand	154-156	3	18
β-strand	160-162	3	17
α-helix	163-165	3
β-strand	166-167	2	17
β-strand	173-181	9	17
α-helix	183-187	5
β-strand	192-197	6	18
β-strand	202-207	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A	protein	231	Bat coronavirus RaTG13	A0ABF7PLN6
1040 heavy chain	H	protein	237	Homo sapiens	P01857 (AlphaFold model)
1040 light chain	L	protein	216	Homo sapiens	P0CG04 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7TTX_1 Spike glycoprotein (chains A)
RVQPTDSIVRFPNITNLCPFGEVFNATTFASVYAWNRKRISNCVADYSVLYNSTSFSTFK
CYGVSPTKLNDLCFTNVYADSFVITGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNS
KHIDAKEGGNFNYLYRLFRKANLKPFERDISTEIYQAGSKPCNGQTGLNCYYPLYRYGFY
PTDGVGHQPYRVVVLSFELLNAPATVCGPKKSTNLVKNKGVNFHHHHHHHH

Sequence of entity 2 (H), FASTA

>7TTX_2 1040 heavy chain (chains H)
QLQLQESGPGLVKPSETLSLTCTVSGGSISSSNFYWGWIRQPPGKGLEWIASITYSGRTF
YNPSLKSRVAISVDTSKNQFSLKLSSVTAADTAVYYCARTFPSYYDRSGYHYLNYGMDVW
GQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 3 (L), FASTA

>7TTX_3 1040 light chain (chains L)
NFMLTQPHSMSESPGKTVTISCTRSSGSIASNYVQWYQQRPGSSPTTVIYEDNQRPSGVP
DRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSSWVFGGGTKLTVLGQPKANPTVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses. Liu, L., Iketani, S., Guo, Y. et al. Sci Transl Med (2022) 14:eabn6859-eabn6859. DOI 10.1126/scitranslmed.abn6859 · PubMed

Other PDB entries of the same protein (UniProt A0ABF7PLN6), best resolution first:

7W6R 2.6 Å, Structure of Bat coronavirus RaTG13 spike receptor-binding domain complexed with its…
9JR4 2.76 Å, Crystal structure of RaTG13 receptor-binding domain complexed with squirrel ACE2
7DRV 3.09 Å, Structural basis of SARS-CoV-2-closely-related bat coronavirus RaTG13 to hACE2
6ZGF 3.1 Å, Spike Protein of RaTG13 Bat Coronavirus in Closed Conformation
9KOS 3.74 Å, Crystal structure of RaTG13 RBD complexed with sheep ACE2
9KOW 3.98 Å, Crystal structure of RaTG13 RBD complexed with cattle ACE2
7P8I 4.5 Å, Receptor-binding domain (RBD) of the spike protein of the bat coronavirus RaTG13 virus…
7P8J 6.58 Å, Receptor-binding domain (RBD) of the spike protein of the bat coronavirus RaTG13 virus…

Browse structure collections

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