7AD1: PDB entry 7AD1

Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G, A892P, A942P and V987P)(One up trimer). Determined by electron microscopy at 2.92 Å resolution. Released 4 Nov 2020.

Method: Electron microscopy
Resolution: 2.92 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Human immunodeficiency virus 1
Chains: 3
Atoms: 21,376
Mol. weight: 434.1 kDa
Ligands: NAG
Released: 4 Nov 2020

Explore 7AD1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7AD1 contains 88 α-helices and 192 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 A: 27 helices, 63 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	1
β-strand	36-37	2	2
β-strand	43	1	3
β-strand	47-55	9	4
β-strand	60-65	6	1
β-strand	84	1	5
β-strand	90-96	7	1
β-strand	103-107	5	5
β-strand	117-122	6	5
β-strand	125-129	5	5
β-strand	169-171	3	5
β-strand	188-197	10	1
β-strand	200-209	10	1
α-helix	217	1
β-strand	222-223	2	2
β-strand	224-229	6	1
β-strand	237-241	5	5
β-strand	265-269	5	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-303	9
β-strand	311-319	9	6
β-strand	324-328	5	7
α-helix	337-340	4
β-strand	349	1	8
α-helix	350-352	3
β-strand	354-358	5	8
β-strand	362	1	9
α-helix	366-370	5
β-strand	376-379	4	8
α-helix	384-389	6
β-strand	392	1	10
β-strand	395-403	9	8
α-helix	404-407	4
α-helix	417-421	5
β-strand	431-437	7	8
β-strand	452-454	3	11
α-helix	460-462	3
β-strand	492-494	3	11
β-strand	507-515	9	8
β-strand	524	1	10
β-strand	525	1	9
β-strand	539-543	5	7
β-strand	546-550	5	7
β-strand	551-554	4	12
β-strand	565-567	3	12
β-strand	573-577	5	12
β-strand	584-588	5	12
α-helix	589-591	3
β-strand	592-599	8	6
β-strand	609-613	5	6
β-strand	642-645	4	6
β-strand	648-651	4	6
β-strand	654-655	2	13
β-strand	664-667	4	13
β-strand	670-675	6	13
β-strand	691-696	6	13
β-strand	702	1	14
β-strand	711-728	18	15
β-strand	734-736	3	16
α-helix	738-743	6
α-helix	747-754	8
α-helix	759-782	24
β-strand	787-790	4	17
α-helix	817-823	7
β-strand	858-860	3	16
α-helix	861-863	3
α-helix	867-884	18
α-helix	887-889	3
α-helix	898-908	11
α-helix	914-918	5
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	15
β-strand	1059-1078	20	15
β-strand	1081-1082	2	18
β-strand	1087-1090	4	18
β-strand	1094-1097	4	15
β-strand	1102-1105	4	15
β-strand	1113-1114	2	15
β-strand	1116	1	19
β-strand	1120-1122	3	18
β-strand	1133-1134	2	18
β-strand	1138	1	19
α-helix	1141-1146	6

Chain B: 28 helices, 62 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	20
β-strand	42-43	2	12
β-strand	47-55	9	21
β-strand	61-64	4	20
β-strand	84-85	2	22
β-strand	89-96	8	20
β-strand	103-107	5	22
β-strand	118-122	5	22
β-strand	125-129	5	22
β-strand	169-170	2	22
β-strand	188-195	8	20
β-strand	201-209	9	20
α-helix	216-218	3
β-strand	225-229	5	20
β-strand	237-241	5	22
β-strand	266-269	4	20
β-strand	271-279	9	21
β-strand	285-290	6	21
α-helix	295-303	9
β-strand	311-319	9	23
α-helix	320-322	3
β-strand	325	1	24
α-helix	338-341	4
β-strand	354-358	5	25
β-strand	361	1	26
α-helix	366-370	5
β-strand	376-379	4	25
β-strand	391-392	2	26
β-strand	395-402	8	25
α-helix	405-409	5
α-helix	418-422	5
β-strand	431-437	7	25
β-strand	448	1	27
β-strand	452-453	2	28
β-strand	493-494	2	28
β-strand	497	1	27
β-strand	508-514	7	25
β-strand	524-525	2	26
β-strand	538-543	6	24
β-strand	546-554	9	24
β-strand	566-567	2	24
β-strand	573-578	6	24
β-strand	581-588	8	24
α-helix	589-591	3
β-strand	592-599	8	23
β-strand	609-613	5	23
β-strand	642-645	4	23
β-strand	648-651	4	23
β-strand	654-655	2	29
β-strand	664-667	4	29
β-strand	670-674	5	29
β-strand	692-696	5	29
β-strand	702	1	30
β-strand	711-715	5	31
β-strand	718-728	11	32
β-strand	734-736	3	33
α-helix	738-743	6
α-helix	748-754	7
α-helix	759-782	24
β-strand	788	1	14
α-helix	807-808	2
α-helix	817-825	9
β-strand	858-860	3	33
α-helix	861-863	3
α-helix	867-884	18
α-helix	887-889	3
α-helix	898-909	12
α-helix	914-918	5
α-helix	920-940	21
α-helix	943-945	3
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	1059-1069	11	32
β-strand	1072-1078	7	31
β-strand	1081-1082	2	34
β-strand	1087-1090	4	34
β-strand	1094-1097	4	31
β-strand	1102-1105	4	31
α-helix	1112	1
β-strand	1113-1114	2	31
α-helix	1115	1
β-strand	1116	1	35
β-strand	1120-1122	3	34
β-strand	1133-1134	2	34
β-strand	1138	1	35
α-helix	1141-1146	6

Chain C: 33 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	36
β-strand	36	1	37
β-strand	43	1	24
β-strand	48-55	8	38
β-strand	60-64	5	36
β-strand	84-85	2	39
β-strand	90-96	7	36
β-strand	103-107	5	39
β-strand	117-122	6	39
β-strand	125-129	5	39
β-strand	169-170	2	39
β-strand	188-197	10	36
β-strand	200-209	10	36
β-strand	222	1	37
β-strand	225-229	5	36
β-strand	237-241	5	39
β-strand	265-269	5	36
β-strand	271-279	9	38
β-strand	285-290	6	38
α-helix	295-303	9
β-strand	311-319	9	40
α-helix	320-322	3
β-strand	324-325	2	41
β-strand	328	1	41
β-strand	335	1	42
α-helix	339-342	4
β-strand	349	1	43
α-helix	350-352	3
β-strand	354-358	5	43
β-strand	362	1	42
α-helix	365-370	6
β-strand	376-379	4	43
α-helix	384-389	6
β-strand	392	1	44
β-strand	394-403	10	43
α-helix	404-409	6
α-helix	417	1
α-helix	418-422	5
β-strand	431-437	7	43
α-helix	439-442	4
β-strand	452-453	2	45
β-strand	493-494	2	45
α-helix	503-505	3
β-strand	507-516	10	43
β-strand	524	1	44
β-strand	525	1	42
β-strand	539-543	5	41
β-strand	546-550	5	41
β-strand	551-554	4	3
β-strand	565-567	3	3
β-strand	573-577	5	3
β-strand	584-588	5	3
α-helix	589-591	3
β-strand	592-599	8	40
β-strand	609-613	5	40
α-helix	617-619	3
β-strand	642-645	4	40
β-strand	648-651	4	40
β-strand	654-655	2	46
β-strand	664-667	4	46
β-strand	670-675	6	46
β-strand	691-696	6	46
β-strand	701-704	4	17
β-strand	711-715	5	47
β-strand	718-728	11	48
β-strand	734-736	3	49
α-helix	738-743	6
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	788	1	30
α-helix	817-824	8
β-strand	858-860	3	49
α-helix	861-863	3
α-helix	867-884	18
α-helix	887-889	3
α-helix	898-908	11
α-helix	914-917	4
α-helix	920-940	21
α-helix	943-945	3
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	48
β-strand	1059-1069	11	48
β-strand	1072-1078	7	47
β-strand	1081-1082	2	50
β-strand	1086-1090	5	50
β-strand	1094-1097	4	47
β-strand	1102-1106	5	47
β-strand	1109-1114	6	47
β-strand	1116	1	51
β-strand	1120-1125	6	50
β-strand	1133-1134	2	50
α-helix	1137	1
β-strand	1138	1	51
α-helix	1139	1
α-helix	1142-1146	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein,Envelope glycoprotein,Spike glycoprotein,Envelope glycoprotein,SARS-CoV-2 S…	A, B, C	protein	1297	Severe acute respiratory syndrome coronavirus 2, Human immunodeficiency virus 1	M1E1E4 (AlphaFold model), P0DTC2 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>7AD1_1 Spike glycoprotein,Envelope glycoprotein,Spike glycoprotein,Envelope glycoprotein,SARS-CoV-2 S protein (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQNVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPSRAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDKPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGSLPETGGGSDY
KDDDDKGGGGSGGGGSGGGGSGGGGSGGGGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

Primary citation

Stabilizing the closed SARS-CoV-2 spike trimer. Juraszek, J., Rutten, L., Blokland, S. et al. Nat Commun (2021) 12:244-244. DOI 10.1038/s41467-020-20321-x · PubMed

Other PDB entries of the same protein (UniProt M1E1E4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BJM 2.07 Å, Crystal Structure of Inhibitor 5c in Complex with Prefusion RSV F Glycoprotein
6VKE 2.1 Å, Crystal Structure of Inhibitor JNJ-40012665 in Complex with Prefusion RSV F Glycoprotein
6A0Z 2.33 Å, Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza…
5KWW 2.5 Å, Crystal Structure of Inhibitor JNJ-53718678 In Complex with Prefusion RSV F Glycoprotein
6VKD 2.5 Å, Crystal Structure of Inhibitor JNJ-36689282 in Complex with Prefusion RSV F Glycoprotein
6VKC 2.6 Å, Crystal Structure of Inhibitor JNJ-36811054 in Complex with Prefusion RSV F Glycoprotein
7ZRV 2.8 Å, cryo-EM structure of omicron spike in complex with de novo designed binder, full map
7QTI 3.04 Å, SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global)
5U68 3.08 Å, Structural basis for antibody cross-neutralization of respiratory syncytial virus and…
6W16 3.1 Å, Crystal structure of a human metapneumovirus monomeric fusion protein complexed with 458…
7FJN 3.25 Å, Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex…
6OUS 3.4 Å, Structure of fusion glycoprotein from human respiratory syncytial virus

Browse structure collections

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