9KWY: SARS-CoV-2 RBD

Cryo-EM structure of SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4. Determined by electron microscopy at 2.82 Å resolution. Released 18 Mar 2026.

Method: Electron microscopy
Resolution: 2.82 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2, Mus musculus
Chains: 4
Atoms: 7,342
Mol. weight: 114.57 kDa
Ligands: NAG
Released: 18 Mar 2026

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

Secondary structure: helices and β-sheets

9KWY contains 42 α-helices and 46 β-strands across 4 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: 32 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	21-52	32
α-helix	56-80	25
α-helix	85-87	3
α-helix	91-101	11
α-helix	110-128	19
α-helix	144-148	5
α-helix	149-153	5
α-helix	158-168	11
α-helix	169-173	5
α-helix	177-193	17
α-helix	199-203	5
α-helix	219-251	33
β-strand	262-263	2	1
α-helix	276-281	6
α-helix	289-290	2
α-helix	294-299	6
α-helix	304-318	15
α-helix	322-324	3
α-helix	325-330	6
β-strand	332	1	2
β-strand	347-352	6	2
β-strand	354-359	6	2
α-helix	367-385	19
α-helix	390-392	3
α-helix	398-412	15
α-helix	415-421	7
α-helix	432-446	15
α-helix	449-465	17
α-helix	473-484	12
β-strand	487-488	2	1
α-helix	500-502	3
α-helix	504-507	4
α-helix	514-533	20
α-helix	548-558	11
α-helix	566-574	9
α-helix	582-587	6
α-helix	589-598	10

Chain B: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	8
β-strand	10-13	4	9
β-strand	19-20	2	10
β-strand	23-29	7	8
β-strand	33-38	6	9
β-strand	45-46	2	9
β-strand	56	1	11
β-strand	58	1	11
β-strand	62-64	3	10
β-strand	68-71	4	8
β-strand	73-75	3	10
α-helix	80-82	3
β-strand	84-90	7	9
β-strand	93	1	3
α-helix	96	1
β-strand	97-98	2	9
β-strand	102-106	5	9

Chain C: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	12
β-strand	10-12	3	13
β-strand	18-21	4	14
β-strand	24-25	2	12
α-helix	29-31	3
β-strand	32	1	15
β-strand	34-39	6	13
β-strand	46-51	6	13
β-strand	58-60	3	13
β-strand	68-72	5	14
β-strand	79-83	5	14
β-strand	92-99	8	13
β-strand	100	1	15
β-strand	106-109	4	13
β-strand	113-117	5	13

Chain G: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	338-342	5
β-strand	344	1	3
β-strand	354-358	5	4
α-helix	365-370	6
β-strand	376-379	4	4
α-helix	386-388	3
β-strand	394-403	10	4
α-helix	404-406	3
α-helix	417	1
α-helix	418-422	5
β-strand	432-437	6	4
β-strand	448	1	5
β-strand	452-454	3	6
α-helix	460-462	3
β-strand	473-474	2	7
β-strand	488-489	2	7
β-strand	492-494	3	6
β-strand	497	1	5
β-strand	507-516	10	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Processed angiotensin-converting enzyme 2	A	protein	581	Homo sapiens	Q56H28 (AlphaFold model)
Spike protein S1	G	protein	186	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
1C4 light chain	B	protein	107	Mus musculus
1C4 heavy chain	C	protein	119	Mus musculus

Sequence of entity 1 (A), FASTA

>9KWY_1 Processed angiotensin-converting enzyme 2 (chains A)
STTEELAKTFLEKFNHEAEELSYQSSLASWNYNTNITDENVQKMNEAGAKWSAFYEEQSK
LAKTYPLAEIHNTTVKRQLQALQQSGSSVLSADKSQRLNTILNAMSTIYSTGKACNPNNP
QECLLLEPGLDDIMENSKDYNERLWAWEGWRAEVGKQLRPLYEEYVALKNEMARANNYED
YGDYWRGDYEEEWTDGYNYSRSQLIKDVEHTFTQIKPLYQHLHAYVRAKLMDTYPSRISP
TGCLPAHLLGDMWGRFWTNLYPLTVPFGQKPNIDVTDAMVNQSWDARRIFKEAEKFFVSV
GLPNMTQGFWENSMLTEPGDSRKVVCHPTAWDLGKGDFRIKMCTKVTMDDFLTAHHEMGH
IQYDMAYAVQPFLLRNGANEGFHEAVGEIMSLSAATPNHLKTIGLLSPGFSEDSETEINF
LLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKEQWMQKWWEMKREIVGVVEPVPHDETYC
DPASLFHVANDYSFIRYYTRTIYQFQFQEALCRIAKHEGPLHKCDISNSSEAGKKLLQML
TLGKSKPWTLALEHVVGEKKMNVTPLLKYFEPLFTWLKEQN

Sequence of entity 2 (G), FASTA

>9KWY_2 Spike protein S1 (chains G)
NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFT
NVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLY
RLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVL
SFELVC

Sequence of entity 3 (B), FASTA

>9KWY_3 1C4 light chain (chains B)
DIVLTQSPATLSVTPGDNVSLSCRASQIISNNLHWYQQKSHESPRLLIKYASQSISGIPS
RFSGSGSGTDFTLSINSVETEDFGMYFCQQSNTWPLTCGSGTKLELN

Sequence of entity 4 (C), FASTA

>9KWY_4 1C4 heavy chain (chains C)
QIQLVQSGPELKKPGETVKISCKASGYTFTDYGLNWVKQAPGKGLKWMGWINTYSGEPTY
NDEFRGRFAFSLETSTITAYLKINNLKNEDTATYFCARGGNWDWYFDVWGAGTTVTVSS

Ligands and cofactors

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

Primary citation

Engineering a multivalent antibody nanoparticle to overcome SARS-CoV-2 Omicron immune evasion. Sun, H., Jiang, Y., Lan, M. et al. PLoS Pathog (2025) 21:e1013744-e1013744. DOI 10.1371/journal.ppat.1013744 · PubMed

Other PDB entries of the same protein (UniProt Q56H28 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9DAK 2.4 Å, Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nathusii ACE2
9N7E 2.5 Å, Eptesicus fuscus ACE2 peptidase domain bound to VsCoV-a7 RBD complex
9C6O 2.77 Å, Merbecovirus MOW15-22 Spike glycoprotein RBD bound to the P. davyi ACE2
7C8D 3.0 Å, Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
8ZUF 3.31 Å, Cryo-EM structure of P.nat ACE2 mutant in complex with MOW15-22 RBD

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