8QH1: Spike glycoprotein

Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody Cv2.3194. Determined by X-ray diffraction at 2.65 Å resolution. Released 19 Jun 2024.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 3
Atoms: 4,753
Mol. weight: 74.92 kDa
Ligands: NAG
Released: 19 Jun 2024

Explore 8QH1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QH1 contains 28 α-helices and 60 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 E: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	334	1
β-strand	335	1	1
α-helix	336	1
α-helix	338-341	4
α-helix	347-348	2
β-strand	349	1	2
α-helix	350-352	3
β-strand	354-358	5	2
β-strand	361-362	2	1
β-strand	376-380	5	2
α-helix	385-389	5
β-strand	392	1	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	452-454	3	3
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	4
β-strand	476	1	5
β-strand	485	1	4
β-strand	488-489	2	4
β-strand	492-494	3	3
β-strand	507-516	10	2
β-strand	524-525	2	1

Chain H: 9 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	27	1	5
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
α-helix	100-102	3
β-strand	104-107	4	8
β-strand	111-113	3	8
β-strand	114-115	2	7
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
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
α-helix	31-33	3
β-strand	34-39	6	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	86-91	6	13
β-strand	94-95	2	13
β-strand	99-103	5	13
β-strand	108	1	14
α-helix	109-110	2
β-strand	111-115	5	15
α-helix	116-118	3
α-helix	119-124	6
β-strand	126-136	11	15
β-strand	137	1	14
β-strand	141-147	7	16
β-strand	150-152	3	16
β-strand	156-160	5	15
α-helix	161-164	4
β-strand	170-179	10	15
α-helix	180-184	5
β-strand	188-195	8	16
β-strand	202-207	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	E	protein	243	Severe acute respiratory syndrome coronavirus 2	A0A8A5XRG7
Cv2.3194 heavy chain	H	protein	229	Homo sapiens
IGK@ protein	L	protein	211	Homo sapiens	Q6PJF2 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>8QH1_1 Spike glycoprotein (chains E)
NITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDL
CFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYN
YRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRV
VVLSFELLHAPATVCGPKGSGLVPRGSHHHHHHHHSAWSHPQFEKGTGGLNDIFEAQKIE
WHE

Sequence of entity 2 (H), FASTA

>8QH1_2 Cv2.3194 heavy chain (chains H)
EVQLVESGGGLIQPGGSLRLSCAASGITVTSNYMSWVRQAPGKGLEWVSVIYPGGSTFYA
DSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDLVVYGMDVWGQGTTVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

Sequence of entity 3 (L), FASTA

>8QH1_3 IGK@ protein (chains L)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIP
GRFSGSGSGTDFTLTISRLEPEDFAIYYCQQGVTFGGGTKVEIKRTVAAPSVFIFPPSDE
QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSK
ADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

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 A0A8A5XRG7), best resolution first:

9AU1 2.41 Å, SARS-CoV-2 XBB.1.5 RBD bound to the VIR-7229 and the S309 Fab fragments
9SSM 2.7 Å, Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD

Browse structure collections

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