8BBO: SARS-CoV-2 Delta-RBD

SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab. Determined by X-ray diffraction at 2.75 Å resolution. Released 22 Mar 2023.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 3
Atoms: 4,752
Mol. weight: 70.45 kDa
Ligands: NAG
Released: 22 Mar 2023

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

Secondary structure: helices and β-sheets

8BBO contains 21 α-helices and 58 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 H: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	11-12	2	6
α-helix	13	1
β-strand	18-25	8	5
β-strand	35-41	7	7
β-strand	48-54	7	7
β-strand	59-61	3	7
α-helix	63-65	3
β-strand	69-74	6	5
β-strand	79-84	6	5
α-helix	89-91	3
β-strand	93-100	8	7
β-strand	108-109	2	7
β-strand	113-115	3	7
β-strand	116-117	2	6
β-strand	123	1	8
α-helix	124-125	2
β-strand	126-130	5	9
β-strand	137-138	2	9
β-strand	141-151	11	9
β-strand	152	1	8
β-strand	157-160	4	10
α-helix	161-163	3
β-strand	165	1	10
β-strand	169-171	3	9
α-helix	172-174	3
β-strand	175-176	2	9
β-strand	182-191	10	9
α-helix	192-194	3
β-strand	200-206	7	10
α-helix	207-209	3
β-strand	211-217	7	10

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-90	6	12
β-strand	96-97	2	12
β-strand	101-105	5	12
β-strand	110	1	13
α-helix	111-112	2
β-strand	113-117	5	14
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	14
β-strand	139	1	13
β-strand	143-149	7	15
β-strand	152-154	3	15
β-strand	158-162	5	14
α-helix	163-166	4
β-strand	172-181	10	14
α-helix	182-185	4
β-strand	190-197	8	15
β-strand	204-209	6	15

Chain R: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	338-342	5
β-strand	349	1	1
β-strand	354-358	5	1
α-helix	365-368	4
β-strand	376-380	5	1
β-strand	395-402	8	1
α-helix	407-409	3
α-helix	418-421	4
β-strand	431-437	7	1
β-strand	448	1	2
β-strand	452-454	3	3
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	4
β-strand	485	1	4
β-strand	488-489	2	4
β-strand	492-494	3	3
β-strand	497	1	2
β-strand	508-514	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	R	protein	202	Severe acute respiratory syndrome coronavirus 2	A0A8B6RM54
IGH@ protein	H	protein	224	Homo sapiens	Q6GMX6 (AlphaFold model)
Immunoglobulin kappa light chain	L	protein	213	Homo sapiens	P0DOX7 (AlphaFold model)

Sequence of entity 1 (R), FASTA

>8BBO_1 Spike glycoprotein (chains R)
HHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTK
LNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVG
GNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQ
PYRVVVLSFELLHAPATVCGKK

Sequence of entity 2 (H), FASTA

>8BBO_2 IGH@ protein (chains H)
QVQLVESGPGRVKPSQTLSLTCTVSGDSINSGINYWNWIRQPAGKELEWIGRIFTSGTTH
YNPSLKSRVTISVDRSKNEFSLTLNSVTAADTAVYFCGRGGTDDYVDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 3 (L), FASTA

>8BBO_3 Immunoglobulin kappa light chain (chains L)
AIQMTQSPSTLSASVGDRVTITCRASQDINSWLAWYQQKPGKAPKLLIYDASSLHSGVPT
RFSGSGSGTEFTLTISSLQPDDFASYYCQQYKSYRTFGRGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses. Dijokaite-Guraliuc, A., Das, R., Zhou, D. et al. Cell Rep (2023) 42:112271-112271. DOI 10.1016/j.celrep.2023.112271 · PubMed

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