7D00: S protein of SARS-CoV-2 in complex

S protein of SARS-CoV-2 in complex bound with FabP5A-1B8. Determined by electron microscopy at 3.0 Å resolution. Released 10 Mar 2021.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 7
Atoms: 30,886
Mol. weight: 586.29 kDa
Ligands: NAG
Released: 10 Mar 2021

Explore 7D00 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7D00 contains 92 α-helices and 286 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: 28 helices, 76 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	47-55	9	4
β-strand	61-65	5	1
β-strand	84-85	2	5
β-strand	90-92	3	6
β-strand	94	1	1
β-strand	95	1	6
β-strand	101	1	7
β-strand	105	1	8
β-strand	106-107	2	5
β-strand	116-121	6	8
β-strand	126-135	10	8
β-strand	141	1	9
β-strand	160-169	10	8
β-strand	189-197	9	6
β-strand	200-208	9	6
α-helix	222	1
β-strand	223	1	2
β-strand	224-230	7	6
β-strand	237-238	2	5
β-strand	242	1	7
β-strand	243	1	9
β-strand	265-267	3	1
β-strand	268-269	2	6
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-303	9
α-helix	308	1
β-strand	309-319	11	10
α-helix	320-322	3
β-strand	323	1	11
β-strand	328	1	11
β-strand	356-358	3	12
β-strand	362	1	13
α-helix	365-369	5
β-strand	376-379	4	12
α-helix	384-389	6
β-strand	391	1	13
β-strand	394-402	9	12
α-helix	407-409	3
α-helix	417-421	5
β-strand	432-437	6	12
α-helix	439-442	4
β-strand	448-454	7	14
α-helix	460-462	3
β-strand	473-474	2	15
β-strand	488-489	2	15
β-strand	492-497	6	14
β-strand	508-516	9	12
β-strand	525	1	13
β-strand	539-543	5	11
β-strand	546-550	5	11
β-strand	551-554	4	16
β-strand	565-567	3	16
β-strand	573-577	5	16
β-strand	584-588	5	16
α-helix	589-591	3
β-strand	592-601	10	10
β-strand	609-613	5	10
β-strand	642-645	4	10
β-strand	648-651	4	10
β-strand	654-655	2	17
β-strand	664-667	4	17
β-strand	670-674	5	17
β-strand	692-696	5	17
α-helix	697-698	2
β-strand	702-704	3	18
β-strand	711-728	18	19
β-strand	733-736	4	20
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	21
β-strand	797	1	22
β-strand	800	1	22
β-strand	807	1	23
α-helix	812-814	3
β-strand	816	1	23
α-helix	817-825	9
β-strand	858-861	4	20
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	19
β-strand	1059-1078	20	19
β-strand	1081-1083	3	24
β-strand	1086-1090	5	24
β-strand	1094-1097	4	19
β-strand	1102-1106	5	19
β-strand	1109-1114	6	19
β-strand	1116	1	25
β-strand	1120-1125	6	24
β-strand	1133-1134	2	24
β-strand	1138	1	25
α-helix	1141-1145	5

Chain B: 21 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	26
β-strand	36-37	2	27
β-strand	42-43	2	16
β-strand	47-55	9	28
β-strand	61-65	5	26
β-strand	84-85	2	29
β-strand	90-95	6	26
β-strand	101-107	7	29
β-strand	116-120	5	29
β-strand	127-131	5	29
β-strand	132	1	30
β-strand	135	1	31
β-strand	141-142	2	32
β-strand	160	1	31
β-strand	164	1	30
β-strand	169-171	3	29
β-strand	188-197	10	26
β-strand	200-209	10	26
β-strand	222-223	2	27
β-strand	224-229	6	26
β-strand	237-242	6	29
β-strand	243-244	2	32
β-strand	265-269	5	26
β-strand	271-279	9	28
β-strand	285-290	6	28
α-helix	295-303	9
β-strand	311-319	9	33
α-helix	320-322	3
β-strand	325	1	34
α-helix	339-342	4
β-strand	348	1	35
β-strand	354-358	5	35
β-strand	361	1	36
α-helix	366-369	4
β-strand	376-380	5	35
β-strand	391-392	2	36
β-strand	395-402	8	35
β-strand	431-436	6	35
β-strand	453	1	37
β-strand	493	1	37
β-strand	508-515	8	35
α-helix	521-522	2
β-strand	524-525	2	36
β-strand	539-543	5	34
β-strand	546-550	5	34
β-strand	551-554	4	38
β-strand	567	1	39
β-strand	573	1	39
β-strand	575-577	3	38
β-strand	584-588	5	38
α-helix	589-591	3
β-strand	592-599	8	33
β-strand	609-613	5	33
β-strand	642-644	3	33
β-strand	648-651	4	33
β-strand	654-655	2	40
β-strand	664-667	4	40
β-strand	670-673	4	40
β-strand	693-696	4	40
α-helix	697-698	2
β-strand	702-704	3	41
β-strand	711-728	18	42
β-strand	733-736	4	43
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	18
α-helix	817-822	6
β-strand	858-861	4	43
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	42
β-strand	1059-1078	20	42
β-strand	1081-1083	3	44
β-strand	1086-1090	5	44
β-strand	1094-1097	4	42
β-strand	1102-1105	4	42
β-strand	1113	1	42
β-strand	1116	1	45
β-strand	1120-1122	3	44
β-strand	1133-1134	2	44
β-strand	1138	1	45
α-helix	1141-1144	4

Chain C: 25 helices, 65 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	46
β-strand	36-37	2	47
β-strand	48-55	8	48
β-strand	60-65	6	46
β-strand	84	1	49
β-strand	89-94	6	46
β-strand	101-107	7	49
β-strand	116-119	4	49
β-strand	128-131	4	49
β-strand	135	1	50
β-strand	160	1	50
β-strand	188-195	8	46
β-strand	201-209	9	46
β-strand	222-223	2	47
β-strand	224-229	6	46
β-strand	237-242	6	49
β-strand	265-269	5	46
β-strand	271-279	9	48
β-strand	285-291	7	48
α-helix	295-303	9
β-strand	311-319	9	51
α-helix	320-322	3
β-strand	325	1	52
β-strand	328	1	52
β-strand	356-358	3	53
β-strand	362	1	54
α-helix	365-369	5
β-strand	376-379	4	53
α-helix	384-389	6
β-strand	391	1	54
β-strand	394-402	9	53
α-helix	407-409	3
α-helix	417-421	5
β-strand	432-437	6	53
α-helix	439-442	4
β-strand	448-454	7	55
α-helix	460-462	3
β-strand	473-474	2	56
β-strand	488-489	2	56
β-strand	492-497	6	55
β-strand	508-516	9	53
β-strand	525	1	54
β-strand	538-543	6	52
β-strand	546-554	9	52
β-strand	565-566	2	3
β-strand	567	1	57
β-strand	573	1	57
β-strand	575-577	3	52
β-strand	584-588	5	52
β-strand	592-599	8	51
β-strand	609-613	5	51
α-helix	617-619	3
β-strand	642-644	3	51
β-strand	648-651	4	51
β-strand	654-655	2	58
β-strand	664-667	4	58
β-strand	670-675	6	58
β-strand	691-696	6	58
β-strand	702-704	3	21
β-strand	711-728	18	59
β-strand	733-736	4	60
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	41
α-helix	817-825	9
β-strand	858-861	4	60
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	59
β-strand	1059-1078	20	59
β-strand	1081-1083	3	61
β-strand	1086-1090	5	61
β-strand	1094-1097	4	59
β-strand	1102-1105	4	59
β-strand	1113	1	59
β-strand	1116	1	62
β-strand	1120-1122	3	61
β-strand	1133-1134	2	61
β-strand	1138	1	62
α-helix	1141-1145	5

Chains H and J: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	63
β-strand	11	1	64
β-strand	17-23	7	63
α-helix	29-31	3
β-strand	33-39	7	65
β-strand	45-51	7	65
β-strand	67-72	6	63
β-strand	77-83	7	63
β-strand	92-98	7	65
β-strand	105	1	65
β-strand	108-109	2	65
β-strand	111	1	64
β-strand	123-126	4	66
β-strand	134	1	66
β-strand	137-147	11	66
β-strand	152-156	5	67
α-helix	157-159	3
β-strand	166-167	2	66
α-helix	168-170	3
β-strand	171-172	2	66
β-strand	178-187	10	66
α-helix	188-190	3
β-strand	197-202	6	67
β-strand	207-212	6	67

Chains K and N: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	68
β-strand	18-23	6	69
β-strand	35-38	4	70
β-strand	44-46	3	70
β-strand	62	1	69
β-strand	65	1	69
β-strand	71-76	6	69
β-strand	85-88	4	70
β-strand	102-103	2	70
β-strand	104-106	3	68
α-helix	112-113	2
β-strand	114-118	5	71
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-137	9	71
β-strand	145-150	6	72
β-strand	153-154	2	72
β-strand	159-163	5	71
α-helix	164-167	4
β-strand	175-182	8	71
α-helix	183-186	4
β-strand	191-197	7	72
β-strand	205-210	6	72

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)
IG c642_heavy_IGHV3-53_IGHD1-26_IGHJ6,chain H of FabP5A-1B8,IGH@ protein	H, J	protein	445	Homo sapiens	A0A5C2GF00 (AlphaFold model), Q6GMX6 (AlphaFold model)
IGL c4203_light_IGKV1-9_IGKJ4,Uncharacterized protein	K, N	protein	214	Homo sapiens	A0A5C2GCZ2 (AlphaFold model), Q8TCD0

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

>7D00_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, J), FASTA

>7D00_2 IG c642_heavy_IGHV3-53_IGHD1-26_IGHJ6,chain H of FabP5A-1B8,IGH@ protein (chains H, J)
EVQLVESGGGLIQPGGSLRLSCAASGFTVSSNYMSWVRQAPGKGLEWVSVIYPGGSTFYA
DSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARETLAFDYWGQGTLVTVSSASTKG
PSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSL
SSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFL
FPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRV
VSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQ
VSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNV
FSCSVMHEALHNHYTQKSLSLSPGK

Sequence of entity 3 (K, N), FASTA

>7D00_3 IGL c4203_light_IGKV1-9_IGKJ4,Uncharacterized protein (chains K, N)
DIQLTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQSGVPS
RFSGSGSGTEFTLTISSLQPEDFATYYCQQLNSYPPAFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	28

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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