7FJN: Spike glycoprotein,Envelope glycoprotein

Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex with two T6 Fab. Determined by electron microscopy at 3.25 Å resolution. Released 27 Apr 2022.

Method: Electron microscopy
Resolution: 3.25 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Human immunodeficiency virus 1, Homo sapiens
Chains: 7
Atoms: 26,824
Mol. weight: 480.89 kDa
Ligands: NAG
Released: 27 Apr 2022

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

Secondary structure: helices and β-sheets

7FJN contains 92 α-helices and 249 β-strands across 7 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: 29 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	37	1	2
β-strand	42-43	2	3
β-strand	48-55	8	4
α-helix	56-57	2
α-helix	60	1
β-strand	61-65	5	1
β-strand	84-85	2	5
β-strand	90-94	5	1
β-strand	103-107	5	5
β-strand	116-122	7	5
β-strand	125-131	7	5
α-helix	139-142	4
β-strand	168-171	4	5
β-strand	188-196	9	1
β-strand	201-209	9	1
β-strand	223	1	2
β-strand	224-229	6	1
β-strand	237-240	4	5
β-strand	265-269	5	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-302	8
β-strand	311-319	9	6
β-strand	325-328	4	7
α-helix	339-341	3
β-strand	349	1	8
β-strand	354-357	4	8
β-strand	376-380	5	8
α-helix	386-388	3
β-strand	392	1	9
β-strand	394-402	9	8
β-strand	431-435	5	8
β-strand	437	1	8
β-strand	452-454	3	10
β-strand	473-474	2	11
β-strand	485	1	11
β-strand	488-489	2	11
β-strand	492-494	3	10
β-strand	508-516	9	8
α-helix	521-522	2
β-strand	524	1	9
β-strand	538-543	6	7
β-strand	546-554	9	7
β-strand	565-567	3	7
β-strand	573-577	5	7
β-strand	584-588	5	7
α-helix	589-591	3
β-strand	592-599	8	6
β-strand	609-613	5	6
α-helix	617-619	3
β-strand	642-645	4	6
β-strand	648-651	4	6
β-strand	654-655	2	12
β-strand	664-667	4	12
β-strand	670-675	6	12
β-strand	691-696	6	12
α-helix	697-698	2
β-strand	702-704	3	13
β-strand	711-715	5	14
β-strand	718-728	11	15
β-strand	734-736	3	16
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	788-790	3	17
β-strand	807	1	18
β-strand	816	1	18
α-helix	817-825	9
β-strand	858-860	3	16
α-helix	861-863	3
α-helix	867-884	18
α-helix	887-889	3
α-helix	898-907	10
α-helix	914-917	4
α-helix	920-940	21
α-helix	942-945	4
α-helix	946-962	17
α-helix	964-967	4
α-helix	977-983	7
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	15
β-strand	1059-1069	11	15
β-strand	1072-1076	5	14
β-strand	1081-1082	2	19
β-strand	1087-1090	4	19
β-strand	1094-1097	4	14
β-strand	1102-1105	4	14
β-strand	1113-1114	2	14
α-helix	1115	1
β-strand	1116	1	20
β-strand	1120-1123	4	19
β-strand	1133-1134	2	19
β-strand	1138	1	20
α-helix	1142-1145	4

Chain B: 26 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	21
β-strand	37	1	22
β-strand	42-43	2	7
β-strand	47-55	9	23
α-helix	56-57	2
β-strand	61-65	5	21
β-strand	84-85	2	24
β-strand	89-94	6	21
β-strand	103-107	5	24
β-strand	116-122	7	24
β-strand	125-131	7	24
α-helix	139-142	4
β-strand	169-171	3	24
β-strand	188-196	9	21
β-strand	201-209	9	21
α-helix	216-217	2
β-strand	223	1	22
β-strand	224-229	6	21
β-strand	237-240	4	24
β-strand	265-269	5	21
β-strand	271-279	9	23
β-strand	285-290	6	23
α-helix	295-303	9
β-strand	311-319	9	25
β-strand	325-328	4	26
α-helix	339-342	4
β-strand	348	1	27
β-strand	356-358	3	27
β-strand	376-380	5	27
β-strand	392	1	28
β-strand	394-402	9	27
β-strand	431-437	7	27
β-strand	452-454	3	29
β-strand	473-474	2	30
β-strand	488-489	2	30
β-strand	492-494	3	29
β-strand	508-516	9	27
α-helix	521-522	2
β-strand	524	1	28
β-strand	538-543	6	26
β-strand	546-554	9	26
β-strand	565-567	3	26
β-strand	573-577	5	26
β-strand	584-588	5	26
α-helix	589-591	3
β-strand	592-599	8	25
β-strand	609-612	4	25
α-helix	617-619	3
β-strand	642-645	4	25
β-strand	648-651	4	25
α-helix	653	1
β-strand	654-655	2	31
β-strand	664-667	4	31
β-strand	670-673	4	31
β-strand	693-696	4	31
α-helix	697-698	2
β-strand	702-704	3	32
β-strand	711-715	5	33
β-strand	718-720	3	34
β-strand	723-728	6	34
β-strand	734-736	3	35
α-helix	738-743	6
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	788-790	3	13
β-strand	807	1	36
β-strand	816	1	36
α-helix	817-825	9
β-strand	858-860	3	35
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-907	10
α-helix	914-917	4
α-helix	920-940	21
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	34
β-strand	1059-1069	11	34
β-strand	1072-1077	6	33
β-strand	1081-1082	2	37
β-strand	1086-1090	5	37
β-strand	1094-1097	4	33
β-strand	1102-1105	4	33
β-strand	1112-1114	3	33
β-strand	1116	1	38
β-strand	1120-1125	6	37
β-strand	1133	1	37
β-strand	1138	1	38
α-helix	1142-1145	4

Chain C: 33 helices, 66 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	39
β-strand	36-37	2	40
β-strand	42-44	3	26
β-strand	48-55	8	41
α-helix	56-57	2
α-helix	60	1
β-strand	61-65	5	39
β-strand	84-85	2	42
β-strand	90-95	6	39
β-strand	103-107	5	42
β-strand	117-121	5	42
β-strand	126-129	4	42
β-strand	169-171	3	42
β-strand	188-197	10	39
β-strand	200-209	10	39
α-helix	216-217	2
β-strand	222-223	2	40
β-strand	224-229	6	39
β-strand	237-240	4	42
β-strand	265-269	5	39
β-strand	271-279	9	41
β-strand	285-290	6	41
α-helix	295-302	8
β-strand	311-319	9	43
α-helix	320-322	3
β-strand	324-328	5	3
β-strand	335	1	44
β-strand	354-358	5	45
β-strand	362	1	44
β-strand	376-380	5	45
α-helix	384-386	3
β-strand	393-403	11	45
α-helix	404-406	3
β-strand	431-435	5	45
β-strand	437	1	45
β-strand	452-454	3	46
α-helix	460-462	3
β-strand	492-494	3	46
β-strand	507-516	10	45
α-helix	531-533	3
β-strand	538-543	6	3
β-strand	546-554	9	3
β-strand	565-567	3	3
β-strand	573-577	5	3
α-helix	583	1
β-strand	584-588	5	3
α-helix	589-591	3
β-strand	592-599	8	43
β-strand	609-613	5	43
α-helix	617-619	3
β-strand	642-645	4	43
β-strand	648-651	4	43
β-strand	654-655	2	47
α-helix	660	1
β-strand	661	1	48
α-helix	662	1
β-strand	664-667	4	47
β-strand	670-675	6	47
β-strand	691-696	6	47
α-helix	697	1
β-strand	698	1	48
β-strand	702-704	3	17
β-strand	711-715	5	49
β-strand	718-728	11	50
β-strand	734-736	3	51
α-helix	738-743	6
α-helix	747-753	7
α-helix	754-759	6
α-helix	761-782	22
β-strand	788-790	3	32
β-strand	807	1	52
β-strand	816	1	52
α-helix	817-825	9
β-strand	858-860	3	51
α-helix	867-884	18
α-helix	887-889	3
α-helix	893-895	3
α-helix	898-907	10
α-helix	914-917	4
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	50
β-strand	1059-1069	11	50
β-strand	1072-1076	5	49
β-strand	1081-1082	2	53
β-strand	1087-1090	4	53
β-strand	1094-1097	4	49
β-strand	1102-1105	4	49
β-strand	1112-1114	3	49
β-strand	1116	1	54
β-strand	1120-1122	3	53
β-strand	1133-1134	2	53
β-strand	1138	1	54
α-helix	1144-1146	3

Chains H and I: 0 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	55
β-strand	18-23	6	56
β-strand	33-39	7	57
β-strand	46-51	6	57
β-strand	59-60	2	57
β-strand	68-73	6	56
β-strand	78-83	6	56
β-strand	93-99	7	57
β-strand	110-112	3	57
β-strand	115	1	55

Chains J and L: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	61
β-strand	10-13	4	62
β-strand	19-25	7	61
β-strand	30-31	2	63
β-strand	36-37	2	63
β-strand	39-44	6	64
β-strand	51-55	5	64
β-strand	59-60	2	64
α-helix	61	1
β-strand	69-73	5	61
β-strand	76-81	6	61
β-strand	91-96	6	64
α-helix	102	1
β-strand	104	1	64
β-strand	108	1	64
β-strand	109-112	4	62

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein,Envelope glycoprotein	A, B, C	protein	1280	Severe acute respiratory syndrome coronavirus 2, Human immunodeficiency virus 1	M1E1E4 (AlphaFold model), P0DTC2 (AlphaFold model)
T6 heavy chain	H, I	protein	117	Homo sapiens
T6 light chain	J, L	protein	113	Homo sapiens

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

>7FJN_1 Spike glycoprotein,Envelope glycoprotein (chains A, B, C)
VNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNG
TKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQF
CNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFK
NIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSSGW
TAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKTFTVEKGIYQTSNF
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFK
CYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNS
NNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQ
PTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKK
FLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCT
EVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQT
NSPGSASSVASQSIIAYTMSLGVENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDC
TMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFG
GFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGL
TVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYE
NQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLN
DILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSK
RVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSN
GTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN
HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPR
DGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGG
SAWSHPQFEKGSDYKDDDDK

Sequence of entity 2 (H, I), FASTA

>7FJN_2 T6 heavy chain (chains H, I)
QVQLQQPGTELVNPGASLKMSCKTSGYRFTSYIIHWVKQTPGQGLEWIGAIFPENDDTSY
SQKFKGKATLTTDTSSSTAYMQLSSLTSEDSAVYYCARDGENVLDYWGQGTSVTVSS

Sequence of entity 3 (J, L), FASTA

>7FJN_3 T6 light chain (chains J, L)
QIVLTQSPSSLAVSVGEKVTLSCKSSQSLLYSNNQKNYLAWYQQKSGRSPKLLLHWTSTR
ESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYYTYPWTFGGGTKLEIK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	25

Primary citation

RBD trimer mRNA vaccine elicits broad and protective immune responses against SARS-CoV-2 variants. Liang, Q., Wang, Y., Zhang, S. et al. iScience (2022) 25:104043-104043. DOI 10.1016/j.isci.2022.104043 · 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
7AD1 2.92 Å, Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G,…
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…
6OUS 3.4 Å, Structure of fusion glycoprotein from human respiratory syncytial virus

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