9AU1: SARS-CoV-2 XBB.1.5 RBD

SARS-CoV-2 XBB.1.5 RBD bound to the VIR-7229 and the S309 Fab fragments. Determined by X-ray diffraction at 2.41 Å resolution. Released 16 Oct 2024.

Method: X-ray diffraction
Resolution: 2.41 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 5
Atoms: 8,190
Mol. weight: 124.04 kDa
Ligands: NAG
Released: 16 Oct 2024

Explore 9AU1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9AU1 contains 44 α-helices and 122 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 H: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	11-12	2	16
β-strand	18-24	7	15
α-helix	28-31	4
β-strand	32	1	17
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	58-60	3	18
β-strand	65	1	15
β-strand	68-73	6	15
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-99	8	18
β-strand	103	1	17
β-strand	104	1	19
β-strand	110-113	4	18
β-strand	117-119	3	18
β-strand	120-121	2	16
β-strand	126	1	20
α-helix	127-128	2
β-strand	129-133	5	21
β-strand	144-154	11	21
β-strand	155	1	20
β-strand	160-163	4	22
α-helix	164-166	3
β-strand	168	1	22
β-strand	172-174	3	21
α-helix	175-177	3
β-strand	178-179	2	21
β-strand	185-194	10	21
α-helix	195-197	3
β-strand	198	1	23
β-strand	201	1	23
β-strand	203-209	7	22
β-strand	214-220	7	22

Chain L: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4	1	24
β-strand	5	1	25
β-strand	9-12	4	26
β-strand	18-23	6	25
β-strand	35-40	6	26
β-strand	47-50	4	26
β-strand	51	1	27
β-strand	55	1	27
β-strand	64-69	6	25
β-strand	72-77	6	25
α-helix	82-84	3
β-strand	86-93	8	26
β-strand	99-101	3	26
β-strand	102	1	24
β-strand	105-109	5	26
β-strand	115	1	28
β-strand	118-122	5	29
α-helix	123-125	3
α-helix	126-130	5
β-strand	134-143	10	29
β-strand	144	1	28
β-strand	149-154	6	30
β-strand	157-159	3	30
β-strand	163-165	3	29
α-helix	166-168	3
β-strand	169-170	2	29
β-strand	176-184	9	29
α-helix	186-190	5
β-strand	195-201	7	30
β-strand	204-210	7	30

Chain M: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	102	1	3
β-strand	109	1	3
β-strand	110	1	4
β-strand	114-117	4	2
β-strand	121-125	5	2
α-helix	128-130	3
β-strand	131	1	5
α-helix	132-133	2
β-strand	134-138	5	6
α-helix	139-140	2
β-strand	141	1	7
β-strand	146	1	8
β-strand	148	1	8
β-strand	149-159	11	6
β-strand	160	1	5
β-strand	165-168	4	9
α-helix	169-171	3
β-strand	178-179	2	6
α-helix	180-182	3
β-strand	183-184	2	6
β-strand	190-199	10	6
α-helix	200-202	3
β-strand	208-214	7	9
α-helix	215-217	3
β-strand	219-225	7	9
β-strand	228	1	7

Chain N: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	11
β-strand	19-25	7	10
α-helix	31-33	3
β-strand	34-39	6	11
β-strand	46-50	5	11
β-strand	54-55	2	11
α-helix	56	1
β-strand	63-68	6	10
β-strand	71-76	6	10
α-helix	81-83	3
β-strand	86-91	6	11
β-strand	97-98	2	11
β-strand	102-106	5	11
β-strand	111	1	12
α-helix	112-113	2
β-strand	114-118	5	13
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	13
β-strand	140	1	12
β-strand	145-150	6	14
β-strand	153-154	2	14
α-helix	155	1
β-strand	159-163	5	13
α-helix	164-167	4
β-strand	173-182	10	13
α-helix	183-188	6
β-strand	191-198	8	14
β-strand	201-208	8	14

Chain R: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	334	1
β-strand	335	1	31
α-helix	336	1
α-helix	338-342	5
β-strand	344	1	4
β-strand	349	1	32
α-helix	350-352	3
β-strand	354-358	5	32
β-strand	361-362	2	31
α-helix	366-369	4
β-strand	375-380	6	32
α-helix	384-387	4
β-strand	392	1	31
β-strand	394-403	10	32
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	32
α-helix	439-442	4
β-strand	448	1	33
β-strand	452-454	3	34
β-strand	457	1	19
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	35
β-strand	485	1	35
β-strand	488-489	2	35
β-strand	492-494	3	34
β-strand	497	1	33
α-helix	503-505	3
β-strand	507-516	10	32
β-strand	524-525	2	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S309 Fab heavy chain	M	protein	230	Homo sapiens
S309 Fab light chain	N	protein	212	Homo sapiens
VIR-7229 Fab heavy chain	H	protein	225	Homo sapiens
VIR-7229 Fab light chain	L	protein	216	Homo sapiens
SARS-CoV-2 XBB.1.5 rbd	R	protein	250	Severe acute respiratory syndrome coronavirus 2	A0A8A5XRG7

Sequence of entity 1 (M), FASTA

>9AU1_1 S309 Fab heavy chain (chains M)
QVQLVQSGAEVKKPGASVKVSCKASGYPFTSYGISWVRQAPGQGLEWMGWISTYNGNTNY
AQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCARDYTRGAWFGESLIGGFDNWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (N), FASTA

>9AU1_2 S309 Fab light chain (chains N)
EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Sequence of entity 3 (H), FASTA

>9AU1_3 VIR-7229 Fab heavy chain (chains H)
EVQLVESGGSVVQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGYIAYDGSDTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVT
VFNQIKPPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 4 (L), FASTA

>9AU1_4 VIR-7229 Fab light chain (chains L)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGV
PDRFSGSKSGNTASLIISGLQAEDEADYYCSSYAGSYIWVFGGGTQLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 5 (R), FASTA

>9AU1_5 SARS-CoV-2 XBB.1.5 RBD (chains R)
MEWSWVFLFFLSVTTGVHSRFPNITNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVI
YNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDD
FTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGPNC
YSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTHHHHHHHHGSGSGLNDI
FEAQKIEWHE

Ligands and cofactors

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

Water and common crystallization additives (EDO, ACY, EPE, K) are not listed.

Primary citation

A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification. Rosen, L.E., Tortorici, M.A., De Marco, A. et al. Cell (2024) 187:7196. DOI 10.1016/j.cell.2024.09.026 · PubMed

Other PDB entries of the same protein (UniProt A0A8A5XRG7), best resolution first:

8QH1 2.65 Å, Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody…
9SSM 2.7 Å, Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD

Browse structure collections

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