8XSF: SARS-CoV-2 rbd + imcas-364 + hACE2

SARS-CoV-2 rbd + imcas-364 + hACE2. Determined by electron microscopy at 2.16 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 2.16 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 4
Atoms: 9,736
Mol. weight: 190.35 kDa
Ligands: ZN, NAG
Released: 17 Jul 2024

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

Secondary structure: helices and β-sheets

8XSF contains 59 α-helices and 68 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: 39 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	21-52	32
α-helix	56-80	25
α-helix	85-87	3
α-helix	91-100	10
α-helix	110-129	20
β-strand	131-133	3	1
α-helix	134	1
β-strand	141-143	3	1
α-helix	144-148	5
α-helix	149-153	5
α-helix	158-171	14
α-helix	173-192	20
α-helix	199-204	6
α-helix	205-207	3
β-strand	209	1	2
β-strand	217	1	2
α-helix	221-251	31
β-strand	260	1	3
β-strand	262-263	2	4
α-helix	264-266	3
α-helix	276-278	3
α-helix	279-282	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	5
β-strand	347-350	4	5
β-strand	356-359	4	5
α-helix	366-384	19
α-helix	390-392	3
α-helix	401-412	12
α-helix	415-419	5
α-helix	432-446	15
α-helix	449-465	17
α-helix	470-472	3
α-helix	473-480	8
α-helix	481-485	5
β-strand	487-488	2	4
α-helix	499-502	4
α-helix	504-507	4
α-helix	514-532	19
α-helix	539-541	3
α-helix	548-558	11
α-helix	566-574	9
α-helix	582-587	6
α-helix	589-598	10
α-helix	599-601	3
β-strand	607	1	3

Chain B: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	350-352	3
β-strand	354-358	5	6
β-strand	361	1	7
α-helix	366-369	4
β-strand	376-380	5	6
β-strand	392	1	7
β-strand	394-403	10	6
α-helix	404-409	6
α-helix	417	1
α-helix	418-422	5
β-strand	431-437	7	6
α-helix	439-442	4
β-strand	448	1	8
β-strand	452-454	3	9
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	10
β-strand	488-489	2	10
β-strand	492-494	3	9
β-strand	497	1	8
β-strand	507-516	10	6
β-strand	524	1	7

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	113-116	4	12
β-strand	120-124	5	12
β-strand	130	1	13
β-strand	133-137	5	14
β-strand	149-158	10	14
β-strand	159	1	13
β-strand	164-167	4	15
α-helix	168-170	3
β-strand	172	1	15
β-strand	176-178	3	14
α-helix	179-181	3
β-strand	182-183	2	14
β-strand	189-197	9	14
α-helix	199-201	3
β-strand	207-213	7	15
β-strand	218-224	7	15

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	16
β-strand	10-13	4	17
β-strand	20-24	5	16
β-strand	33-38	6	17
β-strand	46-49	4	17
β-strand	53-54	2	17
β-strand	63-67	5	16
β-strand	70-74	5	16
β-strand	85-90	6	17
α-helix	96	1
β-strand	98	1	17
β-strand	102-106	5	17
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	153-154	2	20
β-strand	159-163	5	19
α-helix	165-167	3
β-strand	173-182	10	19
α-helix	183-188	6
β-strand	191-197	7	20
β-strand	205-210	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Angiotensin-converting enzyme 2	A	protein	805	Homo sapiens	Q9BYF1 (AlphaFold model)
Spike protein S1	B	protein	209	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
IMCAS-364 H chain	H	protein	456	Homo sapiens
IMCAS-364 L chain	L	protein	215	Homo sapiens

Sequence of entity 1 (A), FASTA

>8XSF_1 Angiotensin-converting enzyme 2 (chains A)
MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQ
NMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTIL
NTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLY
EEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHL
HAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQ
AWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILM
CTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKS
IGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEM
KREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLH
KCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNK
NSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKN
QMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDN
SLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENP
YASIDISKGENNPGFQNTDDVQTSF

Sequence of entity 2 (B), FASTA

>8XSF_2 Spike protein S1 (chains B)
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFK
CYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNS
NNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQ
PTNGVGYQPYRVVVLSFELLHAPATVCGP

Sequence of entity 3 (H), FASTA

>8XSF_3 IMCAS-364 H chain (chains H)
QVQLQESGGGVVQPGRSLRLSCAASGFTFSRYGMHWVRQAPGKGLEWVAVIWYDGSNKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRADDTAVYYCAKQEGTYCSGGSCYSGLDYWGQGT
LVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPA
PELLGGPSVFLFPPKPKGHLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKP
REEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTL
PPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLT
VDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Sequence of entity 4 (L), FASTA

>8XSF_4 IMCAS-364 L chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGIKVDIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1. Tong, Z., Tong, J., Lei, W. et al. Cell Rep (2024) 43:114338-114338. DOI 10.1016/j.celrep.2024.114338 · 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
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…
9UE7 2.27 Å, Cryo-EM structure of SARS-CoV-2 KP.2 spike in complex with ACE2
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

Browse structure collections

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