7E7D: Spike glycoprotein,Collagen alpha-1 chain

Cryo-EM structure of the SARS-CoV-2 wild-type S-Trimer from a subunit vaccine candidate. Determined by electron microscopy at 3.2 Å resolution. Released 24 Mar 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 3
Atoms: 26,509
Mol. weight: 523.12 kDa
Ligands: NAG, ELA
Released: 24 Mar 2021

Explore 7E7D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E7D contains 120 α-helices and 218 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: 40 helices, 73 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	1
β-strand	36-37	2	2
β-strand	43	1	3
β-strand	47-55	9	4
α-helix	56-57	2
β-strand	61-68	8	1
β-strand	78-79	2	1
β-strand	84-85	2	5
β-strand	89-96	8	1
β-strand	101-107	7	5
β-strand	116-121	6	5
β-strand	126-135	10	5
β-strand	141-143	3	6
β-strand	154-156	3	6
β-strand	160-170	11	5
β-strand	188-197	10	1
β-strand	200-209	10	1
β-strand	222-223	2	2
β-strand	224-229	6	1
β-strand	237-242	6	5
β-strand	243-245	3	6
β-strand	262-269	8	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-303	9
β-strand	311-314	4	7
β-strand	325	1	8
β-strand	328	1	8
α-helix	334	1
β-strand	335	1	9
α-helix	336	1
α-helix	338-342	5
α-helix	347-348	2
β-strand	349	1	10
β-strand	354-358	5	10
β-strand	361-362	2	9
α-helix	365-368	4
β-strand	376-380	5	10
α-helix	384-389	6
β-strand	391-392	2	9
β-strand	395-403	9	10
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	10
α-helix	439-442	4
β-strand	448	1	11
β-strand	452-454	3	12
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	13
β-strand	485	1	13
β-strand	488-489	2	13
β-strand	492-494	3	12
β-strand	497	1	11
α-helix	503-505	3
β-strand	507-514	8	10
β-strand	517	1	9
β-strand	524-525	2	9
β-strand	538-543	6	8
β-strand	546-554	9	8
β-strand	565-567	3	8
β-strand	573-577	5	8
β-strand	584-588	5	8
β-strand	594-599	6	7
β-strand	609-613	5	7
α-helix	620-623	4
α-helix	631-638	8
β-strand	642-644	3	7
β-strand	649-651	3	7
β-strand	654-655	2	14
β-strand	664-667	4	14
β-strand	670-675	6	14
β-strand	691-696	6	14
α-helix	697-698	2
β-strand	701-704	4	15
β-strand	711-728	18	16
β-strand	733-736	4	17
α-helix	738	1
α-helix	739-743	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	757-782	26
β-strand	787-789	3	18
α-helix	790-792	3
α-helix	817-825	9
α-helix	827-828	2
α-helix	837-840	4
α-helix	844-847	4
α-helix	849-855	7
β-strand	858-861	4	17
α-helix	862-863	2
α-helix	867-883	17
α-helix	887-890	4
α-helix	898-908	11
α-helix	913-918	6
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	16
β-strand	1059-1078	20	16
β-strand	1081-1082	2	19
β-strand	1087-1090	4	19
β-strand	1094-1097	4	16
β-strand	1102-1105	4	16
β-strand	1113-1114	2	16
β-strand	1116	1	20
β-strand	1120-1122	3	19
β-strand	1133-1134	2	19
β-strand	1138	1	20
α-helix	1141-1146	6

Chain B: 40 helices, 72 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	21
β-strand	36-37	2	22
β-strand	43	1	8
β-strand	47-55	9	23
α-helix	56-57	2
β-strand	61-68	8	21
β-strand	78-79	2	21
β-strand	84-85	2	24
β-strand	89-96	8	21
β-strand	101-107	7	24
β-strand	116-121	6	24
β-strand	126-135	10	24
β-strand	141-143	3	25
β-strand	154-156	3	25
β-strand	160-170	11	24
β-strand	188-197	10	21
β-strand	200-209	10	21
β-strand	222-223	2	22
β-strand	224-229	6	21
β-strand	237-242	6	24
β-strand	243-245	3	25
β-strand	262-269	8	21
β-strand	271-279	9	23
β-strand	285-290	6	23
α-helix	295-303	9
β-strand	311-314	4	26
β-strand	325-328	4	27
α-helix	334	1
β-strand	335	1	28
α-helix	336	1
α-helix	338-342	5
α-helix	347-348	2
β-strand	349	1	29
β-strand	354-358	5	29
β-strand	361-362	2	28
α-helix	365-368	4
β-strand	376-380	5	29
α-helix	384-389	6
β-strand	391-392	2	28
β-strand	395-403	9	29
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	29
α-helix	439-442	4
β-strand	448	1	30
β-strand	452-454	3	31
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	32
β-strand	485	1	32
β-strand	488-489	2	32
β-strand	492-494	3	31
β-strand	497	1	30
α-helix	503-505	3
β-strand	507-514	8	29
β-strand	517	1	28
β-strand	524-525	2	28
β-strand	538-543	6	27
β-strand	546-554	9	27
β-strand	565-567	3	27
β-strand	573-577	5	27
β-strand	584-588	5	27
β-strand	594-599	6	26
β-strand	609-613	5	26
α-helix	617-619	3
α-helix	620-623	4
α-helix	631-638	8
β-strand	642-645	4	26
β-strand	648-651	4	26
β-strand	654-655	2	33
β-strand	664-667	4	33
β-strand	670-675	6	33
β-strand	691-696	6	33
α-helix	697-698	2
β-strand	701-704	4	34
β-strand	711-728	18	35
β-strand	733-736	4	36
α-helix	738	1
α-helix	739-743	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	757-782	26
β-strand	787-790	4	15
α-helix	791-792	2
α-helix	817-825	9
α-helix	827-828	2
α-helix	837-840	4
α-helix	844-847	4
α-helix	849-854	6
β-strand	858-861	4	36
α-helix	862-863	2
α-helix	867-883	17
α-helix	887-890	4
α-helix	898-908	11
α-helix	913-918	6
α-helix	920-940	21
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-983	7
α-helix	986-1032	47
β-strand	1047-1056	10	35
β-strand	1059-1078	20	35
β-strand	1081-1082	2	37
β-strand	1087-1090	4	37
β-strand	1094-1097	4	35
β-strand	1102-1105	4	35
β-strand	1113-1114	2	35
β-strand	1116	1	38
β-strand	1120-1122	3	37
β-strand	1133-1134	2	37
β-strand	1138	1	38
α-helix	1141-1146	6

Chain C: 40 helices, 73 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	39
β-strand	36-37	2	40
β-strand	43	1	27
β-strand	47-55	9	41
α-helix	56-57	2
β-strand	61-68	8	39
β-strand	78-79	2	39
β-strand	84-85	2	42
β-strand	89-96	8	39
β-strand	101-107	7	42
β-strand	116-121	6	42
β-strand	126-135	10	42
β-strand	141-143	3	43
β-strand	154-156	3	43
β-strand	160-170	11	42
β-strand	188-197	10	39
β-strand	200-209	10	39
β-strand	222-223	2	40
β-strand	224-229	6	39
β-strand	237-242	6	42
β-strand	243-245	3	43
β-strand	262-269	8	39
β-strand	271-279	9	41
β-strand	285-290	6	41
α-helix	295-302	8
β-strand	311-314	4	44
β-strand	325	1	3
β-strand	328	1	3
α-helix	334	1
β-strand	335	1	45
α-helix	336	1
α-helix	338-342	5
α-helix	347-348	2
β-strand	349	1	46
β-strand	354-358	5	46
β-strand	361-362	2	45
α-helix	365-368	4
β-strand	376-380	5	46
α-helix	384-389	6
β-strand	391-392	2	45
β-strand	395-403	9	46
α-helix	404-409	6
α-helix	417-421	5
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
β-strand	485	1	49
β-strand	488-489	2	49
β-strand	492-494	3	48
β-strand	497	1	47
α-helix	503-505	3
β-strand	507-514	8	46
β-strand	517	1	45
β-strand	524-525	2	45
β-strand	538-543	6	3
β-strand	546-554	9	3
β-strand	565-567	3	3
β-strand	573-577	5	3
β-strand	584-588	5	3
β-strand	595-599	5	44
β-strand	609-613	5	44
α-helix	620-623	4
α-helix	631-638	8
β-strand	642-645	4	44
β-strand	648-651	4	44
β-strand	654-655	2	50
β-strand	664-667	4	50
β-strand	670-675	6	50
β-strand	691-696	6	50
α-helix	697-698	2
β-strand	701-703	3	18
β-strand	711-728	18	51
β-strand	733-736	4	52
α-helix	738	1
α-helix	739-743	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	757-782	26
β-strand	787-790	4	34
α-helix	791-792	2
α-helix	817-825	9
α-helix	827-828	2
α-helix	837-840	4
α-helix	844-847	4
α-helix	849-854	6
β-strand	858-861	4	52
α-helix	862-863	2
α-helix	867-883	17
α-helix	887-890	4
α-helix	898-908	11
α-helix	913-918	6
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	51
β-strand	1059-1078	20	51
β-strand	1081-1082	2	53
β-strand	1087-1090	4	53
β-strand	1094-1097	4	51
β-strand	1102-1105	4	51
β-strand	1113-1114	2	51
β-strand	1116	1	54
β-strand	1120-1122	3	53
β-strand	1133-1134	2	53
β-strand	1138	1	54
α-helix	1141-1146	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein,Collagen alpha-1(I) chain	A, B, C	protein	1520	Severe acute respiratory syndrome coronavirus 2, Homo sapiens	P02452 (AlphaFold model), P0DTC2 (AlphaFold model)

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

>7E7D_1 Spike glycoprotein,Collagen alpha-1(I) chain (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQYIKRSNGLPGPIGPPGPRGRTGDAGPVGPPGPPGPPGPPGPPSAGFDFSFLP
QPPQEKAHDGGRYYRANDANVVRDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDL
KMCHSDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKR
HVWFGESMTDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQNITYHCKNSVAYMDQQTG
NLKKALLLKGSNEIEIRAEGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKSSRLPIIDV
APLDVGAPDQEFGFDVGPVC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	19
ELA	Elaidic acid	C18 H34 O2	3

Primary citation

Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19. Ma, J., Su, D., Sun, Y. et al. J Virol (2021) 95. DOI 10.1128/JVI.00194-21 · PubMed

Other PDB entries of the same protein (UniProt P02452 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CTD 1.6 Å, Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest…
8YV3 1.68 Å, The heterotrimer structure of peptides derived from human collagen type I
1Q7D 1.8 Å, Structure of the integrin alpha2beta1 binding collagen peptide
5CTI 1.9 Å, Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest…
5CVA 2.1 Å, Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest…
3EJH 2.1 Å, Crystal Structure of the Fibronectin 8-9FnI Domain Pair in Complex with a Type-I…
5K31 2.2 Å, Crystal structure of Human fibrillar procollagen type I C-propeptide Homo-trimer
5CVB 2.25 Å, Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest…
5OU8 2.5 Å, Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)5
5OU9 2.5 Å, Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)3
3GXE 2.6 Å, Complex of a Low Affinity Collagen Site with the Fibronectin 8-9FnI Domain Pair
7E7B 2.6 Å, Cryo-EM structure of the SARS-CoV-2 furin site mutant S-Trimer from a subunit vaccine…

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