7D03: S protein of SARS-CoV-2 in complex

S protein of SARS-CoV-2 in complex bound with FabP5A-2G7. Determined by electron microscopy at 3.2 Å resolution. Released 10 Mar 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 5
Atoms: 27,519
Mol. weight: 515.42 kDa
Ligands: NAG
Released: 10 Mar 2021

Explore 7D03 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7D03 contains 80 α-helices and 247 β-strands across 5 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: 26 helices, 74 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	37	1	2
β-strand	49-55	7	3
β-strand	61-65	5	1
β-strand	84-85	2	4
β-strand	90-92	3	5
β-strand	94	1	1
β-strand	95	1	5
β-strand	101	1	6
β-strand	105	1	7
β-strand	106-107	2	4
β-strand	116-121	6	7
β-strand	126-135	10	7
β-strand	141	1	8
β-strand	160-169	10	7
β-strand	189-197	9	5
β-strand	200-208	9	5
α-helix	222	1
β-strand	223	1	2
β-strand	224-230	7	5
β-strand	237-238	2	4
β-strand	242	1	6
β-strand	243	1	8
β-strand	265-267	3	1
β-strand	268-269	2	5
β-strand	271-279	9	3
β-strand	285-290	6	3
α-helix	295-303	9
α-helix	308-309	2
β-strand	311-319	9	9
β-strand	326-328	3	10
β-strand	356-358	3	11
β-strand	362	1	12
α-helix	365-369	5
β-strand	376-379	4	11
α-helix	384-389	6
β-strand	391	1	12
β-strand	394-402	9	11
α-helix	407-409	3
α-helix	417-421	5
β-strand	432-437	6	11
α-helix	439-442	4
β-strand	448-454	7	13
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	14
β-strand	485	1	14
β-strand	488-489	2	14
β-strand	492-497	6	13
β-strand	508-516	9	11
β-strand	525	1	12
β-strand	541-543	3	10
β-strand	546-548	3	10
β-strand	551-554	4	15
β-strand	566-567	2	15
β-strand	573-577	5	15
β-strand	584-588	5	15
β-strand	592-599	8	9
β-strand	609-613	5	9
β-strand	642-645	4	9
β-strand	648-651	4	9
β-strand	653-655	3	16
β-strand	664-667	4	16
β-strand	670-674	5	16
β-strand	692-696	5	16
β-strand	711-728	18	17
β-strand	733-736	4	18
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	19
β-strand	797	1	20
β-strand	800	1	20
β-strand	807	1	21
α-helix	812-814	3
β-strand	816	1	21
α-helix	817-825	9
β-strand	858-861	4	18
α-helix	862-863	2
α-helix	867-884	18
α-helix	898-908	11
α-helix	913-917	5
α-helix	920-939	20
α-helix	946-963	18
α-helix	977-980	4
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	17
β-strand	1059-1078	20	17
β-strand	1081-1083	3	22
β-strand	1086-1090	5	22
β-strand	1094-1097	4	17
β-strand	1102-1106	5	17
β-strand	1109-1114	6	17
β-strand	1116	1	23
β-strand	1120-1125	6	22
β-strand	1133-1134	2	22
β-strand	1138	1	23
α-helix	1141-1145	5

Chain B: 23 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	24
β-strand	37	1	25
β-strand	43	1	15
β-strand	47-55	9	26
β-strand	61-65	5	24
β-strand	84-85	2	27
β-strand	90-92	3	28
β-strand	94	1	24
β-strand	95	1	28
β-strand	101	1	29
β-strand	105	1	30
β-strand	106-107	2	27
β-strand	116-121	6	30
β-strand	126-135	10	30
β-strand	141	1	31
β-strand	160-169	10	30
β-strand	189-197	9	28
β-strand	200-208	9	28
α-helix	222	1
β-strand	223	1	25
β-strand	224-230	7	28
β-strand	237-238	2	27
β-strand	242	1	29
β-strand	243	1	31
β-strand	265-267	3	24
β-strand	268-269	2	28
β-strand	271-279	9	26
β-strand	285-290	6	26
α-helix	295-303	9
α-helix	308	1
β-strand	309-319	11	32
α-helix	320-322	3
β-strand	323	1	33
β-strand	327	1	33
α-helix	339-342	4
β-strand	348	1	34
β-strand	354-358	5	34
α-helix	366-369	4
β-strand	376-380	5	34
β-strand	391	1	35
β-strand	395-402	8	34
α-helix	417-421	5
β-strand	431-436	6	34
β-strand	453	1	36
β-strand	493	1	36
β-strand	508-512	5	34
α-helix	521-522	2
β-strand	525	1	35
β-strand	539-543	5	33
β-strand	546-550	5	33
β-strand	551-554	4	37
β-strand	566-567	2	37
β-strand	573-577	5	37
β-strand	584-588	5	37
β-strand	592-601	10	32
β-strand	609-613	5	32
β-strand	642-645	4	32
β-strand	648-651	4	32
β-strand	654-655	2	38
β-strand	664-667	4	38
β-strand	670-673	4	38
β-strand	693-696	4	38
α-helix	697-698	2
β-strand	702-704	3	39
β-strand	711-728	18	40
β-strand	733-736	4	41
α-helix	738-742	5
α-helix	748-753	6
α-helix	754-756	3
α-helix	759-782	24
α-helix	817-822	6
β-strand	858-861	4	41
α-helix	862-863	2
α-helix	867-884	18
α-helix	898-908	11
α-helix	914-917	4
α-helix	920-938	19
α-helix	946-964	19
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	40
β-strand	1059-1078	20	40
β-strand	1081-1083	3	42
β-strand	1086-1090	5	42
β-strand	1094-1097	4	40
β-strand	1102-1105	4	40
β-strand	1113	1	40
β-strand	1116	1	43
β-strand	1120-1122	3	42
β-strand	1133-1134	2	42
β-strand	1138	1	43
α-helix	1141-1144	4

Chain C: 23 helices, 65 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	44
β-strand	37	1	45
β-strand	47-55	9	46
β-strand	61-65	5	44
β-strand	84-85	2	47
β-strand	90-92	3	48
β-strand	94	1	44
β-strand	95	1	48
β-strand	101	1	49
β-strand	105	1	50
β-strand	106-107	2	47
β-strand	116-121	6	50
β-strand	126-135	10	50
β-strand	141	1	51
β-strand	160-169	10	50
β-strand	189-197	9	48
β-strand	200-208	9	48
α-helix	222	1
β-strand	223	1	45
β-strand	224-230	7	48
β-strand	237-238	2	47
β-strand	242	1	49
β-strand	243	1	51
β-strand	265-267	3	44
β-strand	268-269	2	48
β-strand	271-279	9	46
β-strand	285-290	6	46
α-helix	295-303	9
α-helix	308-309	2
β-strand	311-316	6	52
β-strand	323	1	53
α-helix	339-342	4
β-strand	348	1	54
β-strand	354-358	5	54
α-helix	365-369	5
β-strand	376-380	5	54
β-strand	395-402	8	54
β-strand	431-436	6	54
β-strand	453	1	55
β-strand	493	1	55
β-strand	508-515	8	54
α-helix	521-522	2
β-strand	539-543	5	53
β-strand	546-550	5	53
β-strand	553-554	2	56
β-strand	576-577	2	56
β-strand	584-586	3	56
α-helix	588-590	3
β-strand	594-599	6	52
β-strand	609-613	5	52
β-strand	642-645	4	52
β-strand	648-651	4	52
β-strand	654-655	2	57
β-strand	664-667	4	57
β-strand	670-673	4	57
β-strand	693-696	4	57
β-strand	702-704	3	19
β-strand	711-728	18	58
β-strand	733-736	4	59
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	39
α-helix	817-825	9
β-strand	858-861	4	59
α-helix	862-863	2
α-helix	867-884	18
α-helix	898-907	10
α-helix	914-917	4
α-helix	920-938	19
α-helix	946-964	19
α-helix	965-967	3
α-helix	978-981	4
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	58
β-strand	1059-1078	20	58
β-strand	1081-1083	3	60
β-strand	1086-1090	5	60
β-strand	1094-1097	4	58
β-strand	1102-1105	4	58
β-strand	1113	1	58
β-strand	1116	1	61
β-strand	1120-1122	3	60
β-strand	1133-1134	2	60
β-strand	1138	1	61
α-helix	1141-1145	5

Chain H: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	62
β-strand	12	1	63
β-strand	17-25	9	62
β-strand	35-41	7	64
β-strand	48-53	6	64
β-strand	59-61	3	64
β-strand	69-74	6	62
β-strand	79-85	7	62
α-helix	89-91	3
β-strand	93-100	8	64
β-strand	122-124	3	64
β-strand	126	1	63
β-strand	135-139	5	65
β-strand	147	1	65
β-strand	150-160	11	65
β-strand	165-169	5	66
α-helix	170-172	3
β-strand	179-180	2	65
α-helix	181-183	3
β-strand	184-185	2	65
β-strand	191-200	10	65
α-helix	201-203	3
β-strand	210-215	6	66
β-strand	220-225	6	66

Chain L: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	67
β-strand	18-23	6	68
β-strand	37-40	4	67
β-strand	47-50	4	67
β-strand	65-69	5	68
β-strand	72-77	6	68
β-strand	87-90	4	67
β-strand	93	1	69
β-strand	100	1	69
β-strand	106-110	5	67
β-strand	119-123	5	70
α-helix	124-126	3
α-helix	127-131	5
β-strand	135-142	8	70
β-strand	150-154	5	71
β-strand	159-160	2	71
β-strand	164-166	3	70
α-helix	167-169	3
β-strand	170-171	2	70
β-strand	177-185	9	70
α-helix	187-192	6
β-strand	196-202	7	71
β-strand	205-211	7	71

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1283	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
Immunoglobulin heavy variable 4-61,chain H of FabP5A-2G7,Epididymis luminal protein 214	H	protein	458	Homo sapiens	A0A0C4DH41 (AlphaFold model), V9HW68 (AlphaFold model)
IGL c2312_light_IGLV2-14_IGLJ2,IGL@ protein	L	protein	217	Homo sapiens	A0A5C2G2G8 (AlphaFold model), Q6IPQ0

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

>7D03_1 Spike glycoprotein (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD
SEPVLKGVKLHYTLEDYKDDDDK

Sequence of entity 2 (H), FASTA

>7D03_2 Immunoglobulin heavy variable 4-61,chain H of FabP5A-2G7,Epididymis luminal protein 214 (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGDSVSSGSYYWSWIRQPPGKGLEWIGYIYYSGSTN
YNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARERCYYGSGRAPRCVWFDPWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPC
PAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKT
KPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVY
TLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSK
LTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Sequence of entity 3 (L), FASTA

>7D03_3 IGL c2312_light_IGLV2-14_IGLJ2,IGL@ protein (chains L)
QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSNRPSGV
SNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTLVVFGGGTKLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	29

Primary citation

Structural basis for bivalent binding and inhibition of SARS-CoV-2 infection by human potent neutralizing antibodies. Yan, R., Wang, R., Ju, B. et al. Cell Res (2021) 31:517-525. DOI 10.1038/s41422-021-00487-9 · PubMed

Other PDB entries of the same protein (UniProt P0DTC2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z8O 0.96 Å, Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
7Y8J 1.03 Å, 3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2
9FC2 1.21 Å, The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the…
7EK6 1.24 Å, Structure of viral peptides IPB19/N52
7EAM 1.4 Å, immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6
7M53 1.4 Å, B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
7M8U 1.45 Å, Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from…
7ZR2 1.45 Å, Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
8D36 1.45 Å, Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody…
8ENS 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail…
8ENW 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike…

Browse structure collections

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