9FC2: SARS-CoV-2 receptor binding domain

The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 4. Determined by X-ray diffraction at 1.21 Å resolution. Released 11 Jun 2025.

Method: X-ray diffraction
Resolution: 1.21 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Camelus dromedarius
Chains: 2
Atoms: 2,965
Mol. weight: 36.9 kDa
Ligands: NAG
Released: 11 Jun 2025

Explore 9FC2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FC2 contains 14 α-helices and 27 β-strands across 2 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: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	334	1
β-strand	335	1	1
α-helix	336	1
α-helix	338-342	5
β-strand	349	1	2
α-helix	350-352	3
β-strand	354-358	5	2
β-strand	361-362	2	1
α-helix	365-370	6
β-strand	376-380	5	2
α-helix	384-389	6
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	452-454	3	3
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	4
β-strand	483-484	2	5
β-strand	485	1	4
β-strand	488-489	2	4
β-strand	492-494	3	3
α-helix	503-505	3
β-strand	507-516	10	2
β-strand	524-525	2	1

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	6
β-strand	10-13	4	5
β-strand	18-26	9	6
β-strand	28-39	12	5
β-strand	46-52	7	5
β-strand	55-59	5	5
β-strand	66-71	6	6
α-helix	72-74	3
β-strand	76-81	6	6
α-helix	86-88	3
β-strand	90-100	11	5
β-strand	107-110	4	5
β-strand	114-119	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	A	protein	207	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
Nanobody 4	B	protein	125	Camelus dromedarius

Sequence of entity 1 (A), FASTA

>9FC2_1 Spike protein S1 (chains A)
GSITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLND
LCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNY
NYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYR
VVVLSFELLHAPATVCGPKKSTNLVPR

Sequence of entity 2 (B), FASTA

>9FC2_2 Nanobody 4 (chains B)
QVQLVESGGGSVQAGGSLRLSCAASGDTGRTCNLVWYRQAPGKELEFVSSISDGSTNYAG
SVKGRFTISQDNAKNTVYLQMNSLKPEDTAVYYCAATISRTGSLWCEEYWGQGTQVTVSS
ALVPR

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, ACT) are not listed.

Primary citation

Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants. Cerdan, L., Silva, K., Rodriguez-Martin, D. et al. MAbs (2025) 17:2499595-2499595. DOI 10.1080/19420862.2025.2499595 · 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
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…
6M1V 1.5 Å, Crystal structure of post fusion core of 2019-nCoV S2 subunit

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