9SSM: 084-7D Fab

Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD. Determined by X-ray diffraction at 2.7 Å resolution. Released 18 Feb 2026.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 4,717
Mol. weight: 76.16 kDa
Ligands: NAG
Released: 18 Feb 2026

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

Secondary structure: helices and β-sheets

9SSM contains 27 α-helices and 59 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
α-helix	96	1
β-strand	100C-103	4	2
β-strand	107-111	5	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
α-helix	125-127	3
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	150-154	5	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-188	3
β-strand	194-200	7	5
α-helix	201-203	3
β-strand	205-211	7	5

Chain K: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-6	3	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	144-150	7	10
β-strand	153-154	2	10
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-198	8	10
β-strand	205-210	6	10

Chain R: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	338-342	5
β-strand	349	1	11
α-helix	350-352	3
β-strand	354-358	5	11
β-strand	361-362	2	12
α-helix	365-369	5
β-strand	376-380	5	11
α-helix	387-389	3
β-strand	391-392	2	12
β-strand	394-403	10	11
α-helix	407-409	3
α-helix	417-421	5
β-strand	431-437	7	11
α-helix	439-442	4
β-strand	448	1	13
β-strand	452-454	3	14
α-helix	460-462	3
β-strand	473-474	2	15
β-strand	485	1	15
β-strand	488-489	2	15
β-strand	492-494	3	14
β-strand	497	1	13
α-helix	503-505	3
β-strand	507-516	10	11
β-strand	524-525	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
084-7D Fab Heavy Chain	H	protein	230	Homo sapiens
084-7D Fab Light Chain	K	protein	214	Homo sapiens
Spike glycoprotein	R	protein	249	Severe acute respiratory syndrome coronavirus 2	A0A8A5XRG7

Sequence of entity 1 (H), FASTA

>9SSM_1 084-7D Fab Heavy Chain (chains H)
EVQLLESGGGLVQPGGSLRLSCAASGFSFSSYAMNWVRQAPGKGLEWVSAISGGGDNIYY
ADSVKGRFTISRDNYKNTLHLQMKSLRAEDTAVYYCAKDHPSWGSSFLNWGQGILVIVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDLEVLFQ

Sequence of entity 2 (K), FASTA

>9SSM_2 084-7D Fab Light Chain (chains K)
DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGRAPKLLIYTASNLESGVPS
RFSGSGSGTEFSLTISSLQPDDFATYYCQQYNSYSLTFGGGTRVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (R), FASTA

>9SSM_3 Spike glycoprotein (chains R)
QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCY
GVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNN
LDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPT
YGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFGGPGHHHHHHHHGGLNDIF
EAQKIEWHE

Ligands and cofactors

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

Primary citation

Defining the mechanism of cross-reactivity for a SARS-CoV-2 Beta-elicited antibody toward omicron sub-lineages. Ayres, F., Lambson, B., Mkhize, N.N. et al. Structure (2026) 34:552. DOI 10.1016/j.str.2026.01.006 · 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
8QH1 2.65 Å, Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody…

Browse structure collections

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