6WPS: SARS-CoV-2 spike glycoprotein

Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment. Determined by electron microscopy at 3.1 Å resolution. Released 27 May 2020.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 9
Atoms: 28,116
Mol. weight: 516.51 kDa
Ligands: NAG
Released: 27 May 2020

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

Secondary structure: helices and β-sheets

6WPS contains 108 α-helices and 282 β-strands across 9 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.

Chains A, B and E: 31 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	36-37	2	2
β-strand	42-43	2	3
β-strand	47-55	9	4
α-helix	56-57	2
β-strand	61-65	5	1
β-strand	83-85	3	5
β-strand	90-96	7	1
β-strand	101-107	7	5
β-strand	117-122	6	5
β-strand	125-131	7	5
α-helix	133-136	4
β-strand	141-142	2	6
β-strand	166-171	6	5
β-strand	188-197	10	1
β-strand	200-209	10	1
α-helix	216-218	3
β-strand	222-223	2	2
β-strand	224-230	7	1
β-strand	237-242	6	5
β-strand	243-244	2	6
β-strand	265-269	5	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-302	8
β-strand	311-319	9	7
α-helix	320-322	3
β-strand	324-328	5	8
α-helix	334	1
β-strand	335	1	9
α-helix	336	1
α-helix	339-342	4
β-strand	344	1	10
β-strand	348-349	2	11
α-helix	350-352	3
β-strand	354-358	5	11
β-strand	361-362	2	9
α-helix	366-370	5
β-strand	376-379	4	11
β-strand	392	1	9
β-strand	394-403	10	11
α-helix	404-409	6
β-strand	431-437	7	11
β-strand	452-453	2	12
β-strand	493-494	2	12
β-strand	507-516	10	11
β-strand	524-525	2	9
α-helix	528-530	3
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
α-helix	589-591	3
β-strand	592-599	8	7
β-strand	609-613	5	7
β-strand	642-645	4	7
β-strand	648-651	4	7
α-helix	653	1
β-strand	654-655	2	13
β-strand	660-661	2	14
β-strand	664-667	4	13
β-strand	670-675	6	13
β-strand	691-696	6	13
β-strand	697-698	2	14
β-strand	701-702	2	15
β-strand	711-728	18	16
β-strand	734-736	3	17
α-helix	738-742	5
α-helix	747-753	7
α-helix	754-759	6
α-helix	761-782	22
β-strand	787-788	2	18
β-strand	807	1	19
β-strand	816	1	19
α-helix	817-823	7
β-strand	858-860	3	17
α-helix	861-863	3
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-907	10
α-helix	913-918	6
α-helix	920-940	21
α-helix	942-945	4
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-981	5
α-helix	986-1028	43
α-helix	1029-1034	6
β-strand	1047-1056	10	16
β-strand	1059-1078	20	16
β-strand	1081-1082	2	20
β-strand	1086-1090	5	20
β-strand	1094-1097	4	16
β-strand	1102-1105	4	16
β-strand	1113	1	16
β-strand	1116	1	21
β-strand	1120-1125	6	20
β-strand	1133-1134	2	20
β-strand	1138	1	21

Chains C, F and H: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	46
β-strand	10	1	47
β-strand	18-25	8	46
α-helix	29-31	3
β-strand	33-39	7	47
β-strand	46-51	6	47
β-strand	58-60	3	47
α-helix	62-64	3
β-strand	68-73	6	46
β-strand	78-83	6	46
α-helix	88-90	3
β-strand	92-99	8	47
β-strand	102	1	48
β-strand	109	1	48
β-strand	110	1	35
β-strand	114-117	4	47
β-strand	121-123	3	47

Chains D, G and L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	49
β-strand	10-11	2	50
β-strand	19-25	7	49
β-strand	34-39	6	50
β-strand	46-50	5	50
β-strand	54-55	2	50
α-helix	56	1
β-strand	63-68	6	49
β-strand	71-76	6	49
α-helix	81-83	3
β-strand	86-91	6	50
β-strand	97-98	2	50
β-strand	102-104	3	50

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
spike glycoprotein	A, B, E	protein	1281	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
S309 neutralizing antibody heavy chain	C, F, H	protein	127	Homo sapiens
S309 neutralizing antibody light chain	D, G, L	protein	107	Homo sapiens

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

>6WPS_1 spike glycoprotein (chains A, B, E)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGTQCVNLTTRTQLPPAYTNSFTRGVYYPDK
VFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNII
RGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYS
SANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFS
ALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNE
NGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEV
FNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFV
IRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNL
KPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAP
ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQT
LEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSN
VFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSLGA
ENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCT
QLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDL
LFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGT
ITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSST
ASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRL
QSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVV
FLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTF
VSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQK
EIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGRENLYFQGGGGSGYIPEAPRDGQAYVR
KDGEWVLLSTFLGHHHHHHHH

Sequence of entity 2 (C, F, H), FASTA

>6WPS_2 S309 neutralizing antibody heavy chain (chains C, F, H)
QVQLVQSGAEVKKPGASVKVSCKASGYPFTSYGISWVRQAPGQGLEWMGWISTYNGNTNY
AQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCARDYTRGAWFGESLIGGFDNWGQG
TLVTVSS

Sequence of entity 3 (D, G, L), FASTA

>6WPS_3 S309 neutralizing antibody light chain (chains D, G, L)
EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	33

Primary citation

Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Pinto, D., Park, Y.J., Beltramello, M. et al. Nature (2020) 583:290-295. DOI 10.1038/s41586-020-2349-y · 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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6WPS is part of these collections:

SARS-CoV-2 and COVID-19

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