6ZXN: SARS-CoV-2 spike protein

Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1). Determined by electron microscopy at 2.93 Å resolution. Released 23 Sept 2020.

Method: Electron microscopy
Resolution: 2.93 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
Chains: 6
Atoms: 28,335
Mol. weight: 483.84 kDa
Ligands: NAG
Released: 23 Sept 2020

Explore 6ZXN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZXN contains 104 α-helices and 268 β-strands across 6 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: 33 helices, 75 β-strands

Element	Residues	Length	Sheet
β-strand	27-31	5	1
β-strand	37	1	2
β-strand	42-43	2	3
β-strand	48-55	8	4
α-helix	56-57	2
β-strand	60-67	8	1
β-strand	84-85	2	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	140-146	7	6
β-strand	151-158	8	6
β-strand	166-171	6	5
α-helix	172-174	3
α-helix	180-182	3
β-strand	188-197	10	1
β-strand	200-209	10	1
α-helix	222	1
β-strand	223	1	2
β-strand	224-229	6	1
β-strand	237-242	6	5
β-strand	243-246	4	6
β-strand	259	1	6
β-strand	263-269	7	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-303	9
β-strand	311-319	9	7
β-strand	326-328	3	8
α-helix	329-331	3
β-strand	335	1	9
α-helix	338-342	5
β-strand	354-358	5	10
β-strand	362	1	9
α-helix	365-369	5
β-strand	376-380	5	10
α-helix	387-389	3
β-strand	392	1	11
β-strand	394-403	10	10
α-helix	404-406	3
α-helix	417	1
α-helix	418-422	5
β-strand	431-437	7	10
α-helix	439-442	4
β-strand	448	1	12
β-strand	452-454	3	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	492-494	3	13
β-strand	497	1	12
β-strand	507-516	10	10
β-strand	524	1	11
β-strand	525	1	9
β-strand	539-543	5	8
β-strand	546-550	5	8
β-strand	551-554	4	15
β-strand	565-568	4	15
β-strand	572-578	7	15
β-strand	583-588	6	15
α-helix	589-591	3
β-strand	592-599	8	7
β-strand	609-613	5	7
β-strand	643-645	3	7
β-strand	648-651	4	7
β-strand	654-655	2	16
β-strand	664-667	4	16
β-strand	670-673	4	16
β-strand	693-696	4	16
α-helix	697-698	2
β-strand	701-704	4	17
β-strand	712-728	17	18
β-strand	733-736	4	19
α-helix	738-742	5
α-helix	747-756	10
α-helix	759-782	24
β-strand	787-790	4	20
α-helix	807-808	2
α-helix	817-824	8
β-strand	858-861	4	19
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-889	3
α-helix	899-909	11
α-helix	913-917	5
α-helix	920-939	20
α-helix	946-965	20
α-helix	977-983	7
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	18
β-strand	1059-1075	17	18
β-strand	1076-1077	2	21
β-strand	1081-1083	3	22
β-strand	1086-1090	5	22
β-strand	1094-1097	4	21
β-strand	1102-1105	4	21
β-strand	1106	1	23
β-strand	1109	1	23
β-strand	1114	1	21
β-strand	1116	1	24
β-strand	1120-1122	3	22
β-strand	1133-1134	2	22
β-strand	1138	1	24
α-helix	1142-1145	4

Chain B: 34 helices, 74 β-strands

Element	Residues	Length	Sheet
α-helix	21-23	3
β-strand	27-31	5	25
β-strand	36-37	2	26
β-strand	42-43	2	15
β-strand	47-55	9	27
α-helix	56-57	2
β-strand	60-67	8	25
β-strand	83-85	3	28
β-strand	90-96	7	25
β-strand	101-107	7	28
β-strand	116-121	6	28
β-strand	126-131	6	28
β-strand	135-146	12	29
β-strand	151-160	10	29
β-strand	168-171	4	28
α-helix	172-174	3
β-strand	188-197	10	25
β-strand	200-209	10	25
β-strand	222-223	2	26
β-strand	224-230	7	25
β-strand	237-242	6	28
β-strand	243-246	4	29
β-strand	259	1	29
β-strand	263-269	7	25
β-strand	271-279	9	27
β-strand	285-290	6	27
α-helix	295-303	9
β-strand	311-319	9	30
β-strand	325-328	4	31
α-helix	334	1
β-strand	335	1	32
α-helix	336	1
α-helix	339-342	4
α-helix	350-352	3
β-strand	354-358	5	33
β-strand	362	1	32
α-helix	365-371	7
β-strand	376-380	5	33
α-helix	384-386	3
β-strand	391-392	2	34
β-strand	394-403	10	33
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	33
α-helix	439-442	4
β-strand	448	1	35
β-strand	452-454	3	36
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	37
β-strand	485	1	37
β-strand	488-489	2	37
β-strand	492-494	3	36
β-strand	497	1	35
β-strand	507-516	10	33
β-strand	524-525	2	34
β-strand	539-543	5	31
β-strand	546-550	5	31
β-strand	551-554	4	38
α-helix	557-560	4
β-strand	565-567	3	38
α-helix	569-571	3
β-strand	573-576	4	38
β-strand	585-588	4	38
α-helix	589-591	3
β-strand	592-599	8	30
β-strand	609-613	5	30
β-strand	642-645	4	30
β-strand	648-651	4	30
β-strand	654-655	2	39
β-strand	664-667	4	39
β-strand	670-673	4	39
β-strand	693-696	4	39
α-helix	697-698	2
β-strand	701	1	40
β-strand	704	1	41
β-strand	711-728	18	42
β-strand	733-736	4	43
α-helix	738-742	5
α-helix	747-754	8
α-helix	759-782	24
β-strand	787-790	4	17
α-helix	807-808	2
α-helix	817-824	8
β-strand	858-861	4	43
α-helix	862-863	2
α-helix	867-884	18
α-helix	898-908	11
α-helix	913-918	6
α-helix	920-939	20
α-helix	946-965	20
α-helix	977-983	7
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1041	1	44
β-strand	1044	1	44
β-strand	1047-1056	10	42
β-strand	1059-1077	19	42
β-strand	1081-1083	3	45
β-strand	1086-1090	5	45
β-strand	1094-1097	4	42
β-strand	1102-1106	5	42
β-strand	1109-1114	6	42
β-strand	1116	1	46
β-strand	1120-1125	6	45
β-strand	1133-1134	2	45
β-strand	1138	1	46
α-helix	1142-1145	4

Chain C: 31 helices, 81 β-strands

Element	Residues	Length	Sheet
β-strand	27-31	5	47
β-strand	37	1	48
β-strand	43	1	38
β-strand	47-55	9	49
α-helix	56-57	2
β-strand	60-67	8	47
β-strand	84-85	2	50
β-strand	90-96	7	47
β-strand	101-107	7	50
β-strand	116-121	6	50
β-strand	126-133	8	50
β-strand	140-146	7	51
β-strand	151-158	8	51
β-strand	163-171	9	50
α-helix	172-174	3
β-strand	186	1	52
β-strand	188-197	10	47
β-strand	200-208	9	47
β-strand	212	1	52
β-strand	223	1	48
β-strand	224-229	6	47
β-strand	237-242	6	50
β-strand	243-246	4	51
β-strand	259	1	51
β-strand	263-269	7	47
β-strand	271-279	9	49
α-helix	280	1
β-strand	285-289	5	49
α-helix	295-303	9
β-strand	311-318	8	53
β-strand	325-327	3	54
β-strand	335	1	55
α-helix	339-342	4
α-helix	350-352	3
β-strand	354-358	5	56
β-strand	362	1	55
α-helix	365-369	5
β-strand	376-381	6	56
β-strand	391-392	2	55
β-strand	395-403	9	56
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	56
α-helix	439-442	4
β-strand	448	1	57
β-strand	452-454	3	58
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	59
β-strand	485	1	59
β-strand	488-489	2	59
β-strand	492-494	3	58
β-strand	497	1	57
β-strand	507-515	9	56
β-strand	524-525	2	55
β-strand	539-543	5	54
β-strand	546-550	5	54
β-strand	551-554	4	3
β-strand	565-567	3	3
α-helix	569-571	3
β-strand	573-576	4	3
β-strand	585-588	4	3
α-helix	589-591	3
β-strand	593-599	7	53
β-strand	609-613	5	53
β-strand	643-645	3	53
β-strand	648-651	4	53
β-strand	654-655	2	60
β-strand	664-667	4	60
β-strand	670-673	4	60
β-strand	693-696	4	60
α-helix	697-698	2
β-strand	701-704	4	20
β-strand	712-728	17	61
β-strand	733-736	4	62
α-helix	738-742	5
α-helix	747-754	8
α-helix	759-782	24
β-strand	787	1	40
β-strand	790	1	41
β-strand	797	1	63
β-strand	800	1	63
β-strand	807	1	64
α-helix	808	1
β-strand	816	1	64
α-helix	817-823	7
β-strand	858-861	4	62
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-889	3
α-helix	898-908	11
α-helix	914-917	4
α-helix	920-940	21
α-helix	946-965	20
α-helix	977-983	7
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	61
β-strand	1059-1075	17	61
β-strand	1076-1077	2	65
β-strand	1081-1083	3	66
β-strand	1086-1090	5	66
β-strand	1094-1097	4	65
β-strand	1102-1105	4	65
β-strand	1106	1	67
β-strand	1109	1	67
β-strand	1114	1	65
β-strand	1116	1	68
β-strand	1120-1122	3	66
β-strand	1133-1134	2	66
β-strand	1138	1	68
α-helix	1142-1145	4

Chain D: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	69
β-strand	8	1	70
β-strand	20-25	6	70
β-strand	27	1	69
β-strand	36-41	6	71
β-strand	48	1	71
β-strand	51-53	3	72
β-strand	60-62	3	72
α-helix	64-66	3
β-strand	70-75	6	70
β-strand	80-85	6	70
α-helix	90-92	3
β-strand	94-100	7	71
β-strand	110	1	71
β-strand	115-116	2	71

Chain E: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	73
β-strand	8	1	74
β-strand	14	1	75
β-strand	20-25	6	74
β-strand	27	1	73
β-strand	36-42	7	76
β-strand	45-53	9	76
β-strand	60-62	3	76
α-helix	64-66	3
β-strand	71-75	5	74
β-strand	80-85	6	74
α-helix	90-92	3
β-strand	94-100	7	76
β-strand	110	1	76
β-strand	115-116	2	76
β-strand	118	1	75

Chain F: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	77
β-strand	20-25	6	78
β-strand	27	1	77
β-strand	35-41	7	79
β-strand	47-53	7	79
β-strand	60-62	3	79
α-helix	64-66	3
β-strand	70-75	6	78
β-strand	80-85	6	78
α-helix	90-92	3
β-strand	94-101	8	79
β-strand	110	1	79
β-strand	115-116	2	79

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1288	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
Nanobody Ty1	D, E, F	protein	134	Vicugna pacos

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

>6ZXN_1 Spike glycoprotein (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAW
SHPQFEKGGGSGGGGSGGSAWSHPQFEK

Sequence of entity 2 (D, E, F), FASTA

>6ZXN_2 Nanobody Ty1 (chains D, E, F)
MAQVQLVETGGGLVQPGGSLRLSCAASGFTFSSVYMNWVRQAPGKGPEWVSRISPNSGNI
GYTDSVKGRFTISRDNAKNTLYLQMNNLKPEDTALYYCAIGLNLSSSSVRGQGTQVTVSS
GGLPETGGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	39

Primary citation

An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction. Hanke, L., Vidakovics Perez, L., Sheward, D.J. et al. Nat Commun (2020) 11:4420-4420. DOI 10.1038/s41467-020-18174-5 · 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…

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6ZXN is part of these collections:

SARS-CoV-2 and COVID-19

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