9UE7: SARS-CoV-2 KP.2 spike

Cryo-EM structure of SARS-CoV-2 KP.2 spike in complex with ACE2. Determined by electron microscopy at 2.27 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 2.27 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 6
Atoms: 39,015
Mol. weight: 652.77 kDa
Released: 24 Dec 2025

Explore 9UE7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9UE7 contains 217 α-helices and 253 β-strands across 6 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: 36 helices, 71 β-strands

Element	Residues	Length	Sheet
β-strand	19-21	3	16
β-strand	37	1	17
β-strand	42-43	2	18
β-strand	47-55	9	19
α-helix	56-57	2
α-helix	62	1
β-strand	63-67	5	16
β-strand	84-85	2	20
β-strand	90-93	4	16
β-strand	101-107	7	20
β-strand	116-121	6	20
β-strand	126-130	5	20
β-strand	135	1	21
β-strand	160	1	21
β-strand	168-171	4	20
α-helix	172-174	3
β-strand	189-197	9	16
β-strand	200-208	9	16
α-helix	222	1
β-strand	223	1	17
β-strand	224-230	7	16
β-strand	237-242	6	20
β-strand	264-269	6	16
β-strand	271-279	9	19
β-strand	285-290	6	19
α-helix	295-303	9
β-strand	311-319	9	22
β-strand	320	1	23
α-helix	321-322	2
β-strand	325	1	24
β-strand	328	1	24
β-strand	335	1	25
α-helix	338-342	5
α-helix	347-349	3
β-strand	354-358	5	26
β-strand	361-362	2	25
α-helix	365-370	6
β-strand	376-380	5	26
α-helix	386-389	4
β-strand	391-392	2	25
β-strand	394-402	9	26
α-helix	417-421	5
β-strand	431-437	7	26
α-helix	439-442	4
β-strand	452-454	3	27
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	28
α-helix	479-480	2
β-strand	485	1	28
β-strand	488-489	2	28
β-strand	492-494	3	27
β-strand	508-516	9	26
β-strand	524-525	2	25
β-strand	538-543	6	24
β-strand	546-554	9	24
β-strand	565-567	3	24
β-strand	573-577	5	24
β-strand	584-588	5	24
α-helix	589-591	3
β-strand	592-599	8	22
β-strand	609-613	5	22
α-helix	617-625	9
β-strand	629	1	23
β-strand	642-644	3	22
β-strand	648-651	4	22
β-strand	654-655	2	29
β-strand	660	1	30
β-strand	664-667	4	29
β-strand	670-676	7	29
β-strand	690-696	7	29
β-strand	697	1	30
α-helix	698	1
β-strand	701-702	2	31
β-strand	711-728	18	32
β-strand	733-736	4	33
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-790	4	34
α-helix	817-825	9
β-strand	858-861	4	33
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-907	10
α-helix	913-918	6
α-helix	920-940	21
α-helix	942-945	4
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-983	7
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	32
β-strand	1059-1078	20	32
β-strand	1081-1083	3	35
β-strand	1086-1090	5	35
β-strand	1094-1097	4	32
β-strand	1102-1105	4	32
β-strand	1113-1114	2	32
β-strand	1116	1	36
β-strand	1120-1125	6	35
β-strand	1133-1134	2	35
β-strand	1138	1	36
α-helix	1140-1146	7

Chain B: 38 helices, 75 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	37
β-strand	37	1	38
β-strand	42-43	2	24
β-strand	48-55	8	39
α-helix	56-57	2
α-helix	62	1
β-strand	63-67	5	37
β-strand	84-85	2	40
β-strand	90-94	5	37
β-strand	103-107	5	40
β-strand	116-121	6	40
β-strand	126-131	6	40
β-strand	135	1	41
β-strand	160	1	41
β-strand	168-171	4	40
α-helix	172-174	3
β-strand	188-197	10	37
β-strand	200-209	10	37
α-helix	222	1
β-strand	223	1	38
β-strand	224-229	6	37
β-strand	237-241	5	40
α-helix	244-246	3
β-strand	263-269	7	37
β-strand	271-279	9	39
β-strand	285-290	6	39
α-helix	295-303	9
α-helix	308-309	2
β-strand	311-319	9	42
β-strand	320	1	43
β-strand	324-325	2	44
β-strand	328	1	44
β-strand	335	1	45
α-helix	339-342	4
α-helix	353	1
β-strand	354-358	5	46
β-strand	361-362	2	45
α-helix	365-369	5
β-strand	375-380	6	46
α-helix	386-389	4
β-strand	391-392	2	45
β-strand	394-402	9	46
α-helix	418-421	4
β-strand	431-437	7	46
α-helix	439-442	4
β-strand	448	1	47
β-strand	452-454	3	48
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	49
α-helix	479-480	2
β-strand	485	1	49
β-strand	488-489	2	49
β-strand	492-494	3	48
β-strand	497	1	47
β-strand	508-516	9	46
β-strand	524-525	2	45
α-helix	531-533	3
β-strand	538-543	6	44
β-strand	546-554	9	44
β-strand	565-567	3	44
β-strand	573-577	5	44
β-strand	584-588	5	44
α-helix	589-591	3
β-strand	592-599	8	42
β-strand	609-613	5	42
α-helix	617-626	10
β-strand	629	1	43
β-strand	642-645	4	42
β-strand	648-651	4	42
β-strand	654-655	2	50
β-strand	664-667	4	50
β-strand	670-676	7	50
β-strand	690-696	7	50
α-helix	697-698	2
β-strand	702-704	3	51
β-strand	711-712	2	52
β-strand	715-728	14	53
β-strand	733-736	4	54
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-788	2	31
β-strand	797	1	55
β-strand	800	1	55
α-helix	817-825	9
β-strand	858-861	4	54
α-helix	862-863	2
α-helix	867-883	17
α-helix	887-890	4
α-helix	898-909	12
α-helix	913-918	6
α-helix	920-939	20
α-helix	942-945	4
α-helix	946-964	19
α-helix	965-967	3
α-helix	979-983	5
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	53
β-strand	1059-1072	14	53
β-strand	1075-1078	4	52
β-strand	1081-1082	2	56
β-strand	1087-1090	4	56
β-strand	1094-1097	4	52
β-strand	1102-1105	4	52
β-strand	1113	1	52
β-strand	1116	1	57
α-helix	1117-1119	3
β-strand	1120-1122	3	56
β-strand	1133-1134	2	56
β-strand	1138	1	57
α-helix	1140-1147	8

Chain C: 34 helices, 74 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	58
β-strand	37	1	59
β-strand	42-43	2	44
β-strand	47-55	9	60
α-helix	56-57	2
α-helix	62	1
β-strand	63-67	5	58
β-strand	84-85	2	61
β-strand	90-94	5	58
β-strand	101-107	7	61
β-strand	116-121	6	61
β-strand	126-131	6	61
β-strand	135	1	62
β-strand	160	1	62
β-strand	168-171	4	61
β-strand	188-197	10	58
β-strand	200-209	10	58
α-helix	222	1
β-strand	223	1	59
β-strand	224-229	6	58
β-strand	237-242	6	61
β-strand	263-269	7	58
β-strand	271-279	9	60
β-strand	285-290	6	60
α-helix	295-303	9
β-strand	311-319	9	63
β-strand	320	1	64
α-helix	321-322	2
β-strand	325	1	18
β-strand	328	1	18
β-strand	335	1	65
α-helix	339-342	4
β-strand	354-358	5	66
β-strand	362	1	65
α-helix	365-370	6
β-strand	375-380	6	66
α-helix	386-389	4
β-strand	391-392	2	65
β-strand	394-402	9	66
α-helix	417-421	5
β-strand	431-437	7	66
α-helix	439-442	4
β-strand	448	1	67
β-strand	452-454	3	68
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	69
α-helix	479-480	2
β-strand	485	1	69
β-strand	488-489	2	69
β-strand	492-494	3	68
β-strand	497	1	67
α-helix	503-505	3
β-strand	508-516	9	66
β-strand	524-525	2	65
β-strand	538-543	6	18
β-strand	546-554	9	18
β-strand	565-567	3	18
β-strand	573-577	5	18
β-strand	584-588	5	18
α-helix	589-591	3
β-strand	592-599	8	63
β-strand	609-613	5	63
α-helix	617-626	10
β-strand	629	1	64
β-strand	642-644	3	63
β-strand	648-651	4	63
β-strand	654-655	2	70
β-strand	664-667	4	70
β-strand	670-675	6	70
β-strand	691-696	6	70
α-helix	697-698	2
β-strand	701-704	4	34
β-strand	712-728	17	71
β-strand	733-736	4	72
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	788-790	3	51
β-strand	797	1	73
β-strand	800	1	73
α-helix	817-825	9
β-strand	858-861	4	72
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-908	11
α-helix	913-918	6
α-helix	920-940	21
α-helix	942-945	4
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-983	7
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	71
β-strand	1059-1075	17	71
β-strand	1076-1078	3	74
β-strand	1081-1082	2	75
β-strand	1086-1090	5	75
β-strand	1094-1097	4	74
β-strand	1102-1105	4	74
β-strand	1113	1	74
β-strand	1116	1	76
β-strand	1120-1125	6	75
β-strand	1133-1134	2	75
β-strand	1138	1	76
α-helix	1140-1147	8

Chain D: 39 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	21-52	32
α-helix	56-79	24
α-helix	80-82	3
α-helix	91-101	11
α-helix	104-107	4
α-helix	110-128	19
β-strand	131-133	3	6
β-strand	141-143	3	6
α-helix	144-149	6
α-helix	150-153	4
α-helix	158-171	14
α-helix	177-193	17
α-helix	199-203	5
α-helix	204-206	3
β-strand	209	1	7
β-strand	217	1	7
α-helix	219-249	31
β-strand	260	1	8
β-strand	262-263	2	9
α-helix	264-266	3
α-helix	276-279	4
α-helix	289-291	3
α-helix	294-299	6
α-helix	304-317	14
α-helix	320-324	5
α-helix	325-330	6
β-strand	332	1	10
β-strand	347-352	6	10
β-strand	355-359	5	10
α-helix	366-384	19
α-helix	385-387	3
α-helix	390-392	3
α-helix	400-412	13
α-helix	415-420	6
α-helix	432-445	14
α-helix	447-449	3
α-helix	450-465	16
α-helix	470-472	3
α-helix	473-480	8
α-helix	481-485	5
β-strand	487-488	2	9
α-helix	500-502	3
α-helix	504-507	4
α-helix	514-532	19
α-helix	548-558	11
α-helix	561-563	3
α-helix	566-574	9
α-helix	582-598	17
α-helix	599-601	3
β-strand	607	1	8

Chain E: 34 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	21-52	32
α-helix	56-79	24
α-helix	80-82	3
α-helix	91-101	11
α-helix	104-107	4
α-helix	110-128	19
β-strand	131-133	3	11
β-strand	141-143	3	11
α-helix	144-149	6
α-helix	150-154	5
α-helix	158-172	15
α-helix	177-193	17
α-helix	199-203	5
α-helix	204-206	3
β-strand	209	1	12
β-strand	217	1	12
α-helix	219-251	33
β-strand	260	1	13
β-strand	262-263	2	14
α-helix	276-279	4
α-helix	289-291	3
α-helix	294-300	7
α-helix	304-317	14
α-helix	325-330	6
β-strand	332	1	15
β-strand	347-352	6	15
β-strand	355-359	5	15
α-helix	366-384	19
α-helix	385-387	3
α-helix	390-392	3
α-helix	400-412	13
α-helix	415-420	6
α-helix	432-443	12
α-helix	447-449	3
α-helix	450-465	16
α-helix	473-484	12
β-strand	487-488	2	14
α-helix	500-502	3
α-helix	504-507	4
α-helix	513-532	20
α-helix	548-558	11
α-helix	561-563	3
α-helix	566-574	9
α-helix	582-599	18
β-strand	607	1	13

Chain F: 36 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	21-52	32
α-helix	56-79	24
α-helix	80-82	3
α-helix	91-101	11
α-helix	104-107	4
α-helix	110-128	19
β-strand	131-133	3	1
β-strand	141-143	3	1
α-helix	144-148	5
α-helix	149-153	5
α-helix	158-171	14
α-helix	177-193	17
α-helix	199-203	5
α-helix	204-206	3
β-strand	209	1	2
β-strand	217	1	2
α-helix	219-251	33
β-strand	260	1	3
α-helix	261	1
β-strand	262-263	2	4
α-helix	276-278	3
α-helix	279-282	4
α-helix	294-300	7
α-helix	304-317	14
α-helix	320-324	5
α-helix	325-330	6
β-strand	332	1	5
α-helix	337-339	3
β-strand	347-350	4	5
β-strand	356-359	4	5
α-helix	366-384	19
α-helix	385-387	3
α-helix	390-392	3
α-helix	400-412	13
α-helix	415-420	6
α-helix	432-445	14
α-helix	447-449	3
α-helix	450-465	16
α-helix	473-484	12
β-strand	487-488	2	4
α-helix	500-502	3
α-helix	504-507	4
α-helix	513-529	17
α-helix	548-558	11
α-helix	566-574	9
α-helix	582-599	18
β-strand	607	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Angiotensin-converting enzyme 2	D, E, F	protein	631	Homo sapiens	Q9BYF1 (AlphaFold model)
Spike glycoprotein	A, B, C	protein	1306	Severe acute respiratory syndrome coronavirus 2	A0A6V7ALX9

Sequence of entity 1 (D, E, F), FASTA

>9UE7_1 Angiotensin-converting enzyme 2 (chains D, E, F)
MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQ
NMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTIL
NTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLY
EEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHL
HAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQ
AWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILM
CTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKS
IGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEM
KREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLH
KCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNK
NSFVGWSTDWSPYADLEVLFQGPHHHHHHHH

Sequence of entity 2 (A, B, C), FASTA

>9UE7_2 Spike glycoprotein (chains A, B, C)
MPMGSLQPLATLYLLGMLVASVLAQCVNLITTTQSYTNSFTRGVYYPDKVFRSSVLHLTQ
DLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKT
QSLLIVNNATNFVIKVCEFQFCNDPFLDVYHKNNKSWMESESGVYSSANNCTFEYVSQPF
LMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIGRDFPQGFSALEPLVDLPIGINIT
RFQTLLALNRSYLTPGDSSSGWTAGAADYYVGYLQPRTFLLKYNENGTITDAVDCALDPL
SETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNVTNLCPFHEVFNATTFASVYAWNRT
RISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTG
NIADYNYKLPDDFTGCVIAWNSNKLDSKHSGNYDYWYRSLRKSKLKPFERDISTEIYQAG
NKPCKGKGPNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNK
CVNFNFNGLTGTGVLTKSNKKFLPFQQFGRDIVDTTDAVRDPQTLEILDITPCSFGGVSV
ITPGTNTSNQVAVLYQGVNCTEVSVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVN
NSYECDIPIGAGVCASYQTQTKSRGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTN
FTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKN
TQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQY
GDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIP
FPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLFSTPSALGKLQDVVNHNAQ
ALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAE
IRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTT
APAICHDGKAHFPREGVFVSNGTHWFLTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTV
YDPLQLELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESL
IDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVFLSTFLSGLEVLFQGPGGWSHPQFEK
GGGSGGGSGGSAWSHPQFEKGGSGLNDIFEAQKIEWHEHHHHHHHH

Primary citation

Pathogenicity, virological features, and immune evasion of SARS-CoV-2 JN.1-derived variants including JN.1.7, KP.2, KP.3, and KP.3.1.1. Shi, J., Zhao, X., Jin, X. et al. Nat Commun (2025) 16:11002-11002. DOI 10.1038/s41467-025-66018-x · PubMed

Other PDB entries of the same protein (UniProt Q9BYF1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SPA 1.79 Å, Apo ACE2 extracellular domain
28KD 2.02 Å, ACE2 extracellular domain in complex with the macrocyclic peptide GR3.1.2
8BYJ 2.07 Å, The structures of Ace2 in complex with bicyclic peptide inhibitor
8B9P 2.11 Å, ACE2 in complex with bicyclic peptide inhibitor
8XSF 2.16 Å, SARS-CoV-2 rbd + imcas-364 + hACE2
1R42 2.2 Å, Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2)
7JVO 2.2 Å, Importin alpha bound to the C-terminus of ACE2
8TOR 2.2 Å, ACE2-peptide 2 complex
9RVA 2.2 Å, Crystal structure of the extracellular part of human ACE2 in complex with the…
8TOQ 2.3 Å, ACE2-peptide 1 complex
8BFW 2.33 Å, The structures of Ace2 in complex with bicyclic peptide inhibitor
8TOS 2.35 Å, ACE2-peptide 6 complex

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