8QH0: SARS-CoV-2 RBD with the antibody Cv2.3194

Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194. Determined by X-ray diffraction at 1.87 Å resolution. Released 19 Jun 2024.

Method: X-ray diffraction
Resolution: 1.87 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 3
Atoms: 5,154
Mol. weight: 70.99 kDa
Ligands: PRO
Released: 19 Jun 2024

Explore 8QH0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QH0 contains 28 α-helices and 61 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: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	335	1	1
α-helix	339-342	4
β-strand	349	1	2
α-helix	350-352	3
β-strand	354-358	5	2
β-strand	361-362	2	1
α-helix	366-369	4
β-strand	376-380	5	2
α-helix	387-389	3
β-strand	391-392	2	1
β-strand	394-403	10	2
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	2
α-helix	439-442	4
β-strand	448	1	3
β-strand	452-454	3	4
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	5
β-strand	485	1	5
β-strand	488-489	2	5
β-strand	492-494	3	4
β-strand	497	1	3
α-helix	503-505	3
β-strand	507-516	10	2
β-strand	524-525	2	1

Chain H: 10 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
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	87-89	3
β-strand	91-98	8	8
β-strand	104-107	4	8
β-strand	111-113	3	8
β-strand	114-115	2	7
α-helix	118-120	3
β-strand	121	1	9
α-helix	122-123	2
β-strand	124-128	5	10
α-helix	129-131	3
β-strand	139-149	11	10
β-strand	150	1	9
β-strand	155-158	4	11
α-helix	159-161	3
β-strand	163	1	11
β-strand	167-169	3	10
α-helix	170-172	3
β-strand	173-174	2	10
β-strand	180-189	10	10
α-helix	190-192	3
β-strand	198-204	7	11
α-helix	205-207	3
β-strand	209-215	7	11

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	35-39	5	13
β-strand	46-50	5	13
β-strand	54-55	2	13
α-helix	56	1
β-strand	63-68	6	12
β-strand	71-76	6	12
α-helix	81-83	3
β-strand	85-91	7	13
β-strand	94-95	2	13
β-strand	99-103	5	13
β-strand	112	1	14
α-helix	113-114	2
β-strand	115-119	5	15
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	15
β-strand	141	1	14
β-strand	146-151	6	16
β-strand	154-155	2	16
α-helix	156	1
β-strand	160-164	5	15
α-helix	165-168	4
β-strand	174-183	10	15
α-helix	184-188	5
β-strand	192-198	7	16
β-strand	206-211	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	A	protein	206	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
Cv2.3194 Heavy chain	H	protein	229	Homo sapiens
IGK@ protein	L	protein	211	Homo sapiens	Q6PJF2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8QH0_1 Spike protein S1 (chains A)
NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSFLYNSASFSTFKCYGVSPTKLNDL
CFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYN
YLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRV
VVLSFELLHAPATVCGPKGSGDDDDK

Sequence of entity 2 (H), FASTA

>8QH0_2 Cv2.3194 Heavy chain (chains H)
EVQLVESGGGLIQPGGSLRLSCAASGITVTSNYMSWVRQAPGKGLEWVSVIYPGGSTFYA
DSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDLVVYGMDVWGQGTTVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

Sequence of entity 3 (L), FASTA

>8QH0_3 IGK@ protein (chains L)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIP
GRFSGSGSGTDFTLTISRLEPEDFAIYYCQQGVTFGGGTKVEIKRTVAAPSVFIFPPSDE
QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSK
ADYEKHKVYACEVTHQGLSSPVTKSFNRGEN

Ligands and cofactors

ID	Name	Formula	Copies
PRO	Proline	C5 H9 N O2	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2. Planchais, C., Fernandez, I., Chalopin, B. et al. iScience (2024) 27:110354-110354. DOI 10.1016/j.isci.2024.110354 · PubMed

Other PDB entries of the same protein (UniProt P0DTC2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z8O 0.96 Å, Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
7Y8J 1.03 Å, 3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2
9FC2 1.21 Å, The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the…
7EK6 1.24 Å, Structure of viral peptides IPB19/N52
7EAM 1.4 Å, immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6
7M53 1.4 Å, B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
7M8U 1.45 Å, Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from…
7ZR2 1.45 Å, Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
8D36 1.45 Å, Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody…
8ENS 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail…
8ENW 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike…

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