7E7B: Spike glycoprotein,Collagen alpha-1 chain

Cryo-EM structure of the SARS-CoV-2 furin site mutant S-Trimer from a subunit vaccine candidate. Determined by electron microscopy at 2.6 Å resolution. Released 24 Mar 2021.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 3
Atoms: 27,363
Mol. weight: 526.77 kDa
Ligands: NAG, ELA, VCG
Released: 24 Mar 2021

Explore 7E7B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E7B contains 117 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: 39 helices, 72 β-strands

Element	Residues	Length	Sheet
α-helix	21-23	3
α-helix	25-26	2
β-strand	27-31	5	1
β-strand	37	1	2
β-strand	43	1	3
β-strand	47-55	9	4
α-helix	56-57	2
β-strand	60-68	9	1
β-strand	78-79	2	1
β-strand	83-85	3	5
β-strand	90-96	7	1
β-strand	101-107	7	5
β-strand	116-121	6	5
β-strand	126-131	6	5
β-strand	133-135	3	6
β-strand	140-146	7	5
β-strand	151-156	6	5
β-strand	160-163	4	6
β-strand	168-171	4	5
β-strand	186-197	12	1
β-strand	200-212	13	1
α-helix	216-218	3
β-strand	223	1	2
β-strand	224-229	6	1
β-strand	237-246	10	5
β-strand	259	1	5
β-strand	263-269	7	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-302	8
β-strand	311-315	5	7
α-helix	316-318	3
β-strand	324-325	2	8
β-strand	328	1	8
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	362	1	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	452-454	3	11
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	12
β-strand	485	1	12
β-strand	488-489	2	12
β-strand	492-494	3	11
α-helix	503-505	3
β-strand	507-514	8	10
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	595-599	5	7
β-strand	609-612	4	7
β-strand	642-645	4	7
β-strand	648-651	4	7
β-strand	654-660	7	13
β-strand	664-667	4	13
β-strand	670-675	6	13
β-strand	691-697	7	13
α-helix	698	1
β-strand	701-704	4	14
β-strand	711-728	18	15
β-strand	733-736	4	16
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	17
α-helix	791-792	2
α-helix	817-825	9
α-helix	844-847	4
α-helix	849-854	6
β-strand	858-861	4	16
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	988-1028	41
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	1142-1145	4

Chain B: 39 helices, 73 β-strands

Element	Residues	Length	Sheet
α-helix	21-23	3
α-helix	25-26	2
β-strand	27-31	5	20
β-strand	37	1	21
β-strand	43	1	8
β-strand	47-55	9	22
α-helix	56-57	2
β-strand	60-68	9	20
β-strand	78-79	2	20
β-strand	83-85	3	23
β-strand	90-96	7	20
β-strand	101-107	7	23
β-strand	116-121	6	23
β-strand	126-131	6	23
β-strand	133-135	3	24
β-strand	140-146	7	23
β-strand	151-156	6	23
β-strand	160-163	4	24
β-strand	168-171	4	23
β-strand	186-197	12	20
β-strand	200-212	13	20
α-helix	216-218	3
β-strand	223	1	21
β-strand	224-229	6	20
β-strand	237-246	10	23
β-strand	259	1	23
β-strand	263-269	7	20
β-strand	271-279	9	22
β-strand	285-290	6	22
α-helix	295-302	8
β-strand	311-315	5	25
α-helix	316-318	3
β-strand	324-325	2	26
β-strand	328	1	26
β-strand	335	1	27
α-helix	336	1
α-helix	338-342	5
α-helix	347-348	2
β-strand	349	1	28
β-strand	354-358	5	28
β-strand	361-362	2	27
α-helix	365-368	4
β-strand	376-380	5	28
α-helix	384-389	6
β-strand	391-392	2	27
β-strand	395-403	9	28
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	28
α-helix	439-442	4
β-strand	452-454	3	29
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	30
β-strand	485	1	30
β-strand	488-489	2	30
β-strand	492-494	3	29
α-helix	503-505	3
β-strand	507-514	8	28
β-strand	517	1	27
β-strand	524-525	2	27
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
β-strand	595-599	5	25
β-strand	609-612	4	25
β-strand	642-645	4	25
β-strand	648-651	4	25
β-strand	654-660	7	31
β-strand	664-667	4	31
β-strand	670-675	6	31
β-strand	691-697	7	31
α-helix	698	1
β-strand	701-704	4	32
β-strand	711-728	18	33
β-strand	733-736	4	34
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	14
α-helix	791-792	2
α-helix	817-825	9
α-helix	844-847	4
α-helix	849-854	6
β-strand	858-861	4	34
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	988-1028	41
α-helix	1029-1033	5
β-strand	1047-1056	10	33
β-strand	1059-1078	20	33
β-strand	1081-1082	2	35
β-strand	1087-1090	4	35
β-strand	1094-1097	4	33
β-strand	1102-1105	4	33
β-strand	1113-1114	2	33
β-strand	1116	1	36
β-strand	1120-1122	3	35
β-strand	1133-1134	2	35
β-strand	1138	1	36
α-helix	1142-1145	4

Chain C: 39 helices, 73 β-strands

Element	Residues	Length	Sheet
α-helix	21-23	3
α-helix	25-26	2
β-strand	27-31	5	37
β-strand	37	1	38
β-strand	43	1	26
β-strand	47-55	9	39
β-strand	60-68	9	37
β-strand	78-79	2	37
β-strand	83-85	3	40
β-strand	90-96	7	37
β-strand	101-107	7	40
β-strand	116-121	6	40
β-strand	126-131	6	40
β-strand	133-135	3	41
β-strand	140-146	7	40
β-strand	151-156	6	40
β-strand	160-163	4	41
β-strand	168-171	4	40
β-strand	186-197	12	37
β-strand	200-212	13	37
α-helix	216-218	3
β-strand	223	1	38
β-strand	224-229	6	37
β-strand	237-246	10	40
β-strand	259	1	40
β-strand	263-269	7	37
β-strand	271-279	9	39
β-strand	285-290	6	39
α-helix	295-302	8
β-strand	311-315	5	42
α-helix	316-318	3
β-strand	324-325	2	3
β-strand	328	1	3
β-strand	335	1	43
α-helix	336	1
α-helix	338-342	5
α-helix	347-348	2
β-strand	349	1	44
β-strand	354-358	5	44
β-strand	361-362	2	43
α-helix	365-368	4
β-strand	376-380	5	44
α-helix	384-389	6
β-strand	391-392	2	43
β-strand	395-403	9	44
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	44
α-helix	439-442	4
β-strand	452-454	3	45
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	46
β-strand	485	1	46
β-strand	488-489	2	46
β-strand	492-494	3	45
α-helix	503-505	3
β-strand	507-514	8	44
β-strand	517	1	43
β-strand	524-525	2	43
α-helix	528-530	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
β-strand	584-588	5	3
β-strand	595-599	5	42
β-strand	609-612	4	42
β-strand	642-645	4	42
β-strand	648-651	4	42
β-strand	654-660	7	47
β-strand	664-667	4	47
β-strand	670-675	6	47
β-strand	691-697	7	47
α-helix	698	1
β-strand	701-704	4	17
β-strand	711-728	18	48
β-strand	733-736	4	49
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	32
α-helix	791-792	2
α-helix	817-825	9
α-helix	844-847	4
α-helix	849-854	6
β-strand	858-861	4	49
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	988-1028	41
α-helix	1029-1033	5
β-strand	1047-1056	10	48
β-strand	1059-1078	20	48
β-strand	1081-1082	2	50
β-strand	1087-1090	4	50
β-strand	1094-1097	4	48
β-strand	1102-1105	4	48
β-strand	1113-1114	2	48
β-strand	1116	1	51
β-strand	1120-1122	3	50
β-strand	1133-1134	2	50
β-strand	1138	1	51
α-helix	1142-1145	4

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

>7E7B_1 Spike glycoprotein,Collagen alpha-1(I) chain (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPRRAASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
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	15
ELA	Elaidic acid	C18 H34 O2	3
VCG	2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl…	C32 H60 O10	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
7E7D 3.2 Å, Cryo-EM structure of the SARS-CoV-2 wild-type S-Trimer from a subunit vaccine candidate

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