7ZSS: D614 spike

cryo-EM structure of D614 spike in complex with de novo designed binder. Determined by electron microscopy at 2.63 Å resolution. Released 1 Mar 2023.

Method: Electron microscopy
Resolution: 2.63 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Drosophila melanogaster
Chains: 6
Atoms: 25,942
Mol. weight: 416.46 kDa
Ligands: NAG
Released: 1 Mar 2023

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

Secondary structure: helices and β-sheets

7ZSS contains 85 α-helices and 187 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: 27 helices, 63 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	1
β-strand	36-37	2	2
β-strand	42-43	2	3
β-strand	48-55	8	4
α-helix	56-57	2
β-strand	60-65	6	1
β-strand	84-85	2	5
β-strand	90-92	3	1
β-strand	104-107	4	5
β-strand	118-121	4	5
β-strand	126-129	4	5
β-strand	132	1	6
β-strand	164	1	6
β-strand	169-172	4	5
β-strand	191-197	7	1
β-strand	200-206	7	1
β-strand	222-223	2	2
β-strand	224-230	7	1
β-strand	237-240	4	5
β-strand	265-269	5	1
β-strand	271-279	9	4
β-strand	285-290	6	4
α-helix	295-303	9
β-strand	311-319	9	7
α-helix	320-322	3
β-strand	325-328	4	8
α-helix	338-342	5
β-strand	356-358	3	9
β-strand	362	1	10
β-strand	376-379	4	9
β-strand	395-402	8	9
α-helix	407-410	4
α-helix	417-421	5
β-strand	432-437	6	9
β-strand	452-454	3	11
α-helix	460-462	3
β-strand	492-494	3	11
β-strand	508-513	6	9
β-strand	525	1	10
β-strand	538-543	6	8
β-strand	546-554	9	8
β-strand	565-567	3	12
β-strand	573-576	4	12
β-strand	577	1	13
β-strand	584	1	13
β-strand	585-588	4	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
β-strand	654-660	7	14
β-strand	664-667	4	14
β-strand	670-674	5	14
β-strand	692-697	6	14
β-strand	701-703	3	15
β-strand	711-728	18	16
β-strand	733-736	4	17
α-helix	738	1
α-helix	739-743	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-789	3	18
α-helix	817-825	9
β-strand	858-861	4	17
α-helix	862-863	2
α-helix	867-884	18
α-helix	887-890	4
α-helix	898-909	12
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	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1055	9	16
β-strand	1059-1078	20	16
β-strand	1081-1082	2	19
β-strand	1087-1090	4	19
β-strand	1094-1097	4	16
β-strand	1102-1105	4	16
β-strand	1113	1	16
β-strand	1116	1	20
α-helix	1117-1119	3
β-strand	1120-1122	3	19
β-strand	1133-1134	2	19
β-strand	1138	1	20
α-helix	1141-1145	5

Chain B: 26 helices, 64 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	21
β-strand	36-37	2	22
β-strand	42-43	2	12
β-strand	48-55	8	23
α-helix	56-57	2
β-strand	60-63	4	21
β-strand	65	1	24
β-strand	84-85	2	25
β-strand	90-94	5	24
β-strand	103-107	5	25
β-strand	117-121	5	25
β-strand	126-129	4	25
β-strand	132	1	26
β-strand	140	1	27
β-strand	164	1	26
β-strand	169-172	4	25
β-strand	191-197	7	24
β-strand	200-206	7	24
β-strand	222-223	2	22
β-strand	224-229	6	24
β-strand	237-241	5	25
β-strand	242	1	27
β-strand	265-269	5	24
β-strand	271-279	9	23
β-strand	285-290	6	23
α-helix	295-303	9
β-strand	311-318	8	28
α-helix	320-322	3
β-strand	325-328	4	29
α-helix	338-341	4
β-strand	354-358	5	30
β-strand	362	1	31
β-strand	376-379	4	30
α-helix	387-389	3
β-strand	393-403	11	30
α-helix	407-410	4
α-helix	417-421	5
β-strand	430-437	8	30
β-strand	453-454	2	32
α-helix	460-462	3
β-strand	492-493	2	32
β-strand	507-516	10	30
β-strand	525	1	31
β-strand	538-543	6	29
β-strand	546-554	9	29
β-strand	565-567	3	29
β-strand	573-577	5	29
β-strand	584-588	5	29
β-strand	593-599	7	28
β-strand	609-613	5	28
α-helix	634-637	4
β-strand	642-644	3	28
β-strand	648-651	4	28
β-strand	654-655	2	33
β-strand	664-667	4	33
β-strand	670-673	4	33
β-strand	693-696	4	33
α-helix	697-698	2
β-strand	701-704	4	34
β-strand	711-728	18	35
β-strand	733-736	4	36
α-helix	739-743	5
α-helix	747-753	7
α-helix	754-756	3
α-helix	759-782	24
β-strand	787-789	3	15
α-helix	817-825	9
β-strand	858-861	4	36
α-helix	862-863	2
α-helix	867-884	18
α-helix	898-909	12
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	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1055	9	35
β-strand	1059-1076	18	35
β-strand	1081-1083	3	37
β-strand	1086-1090	5	37
β-strand	1094-1097	4	35
β-strand	1102-1105	4	35
β-strand	1113	1	35
β-strand	1116	1	38
β-strand	1120-1122	3	37
β-strand	1133-1134	2	37
β-strand	1138	1	38
α-helix	1141-1145	5

Chain C: 26 helices, 60 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	39
β-strand	37	1	40
β-strand	42-43	2	29
β-strand	48-55	8	41
β-strand	60-63	4	39
β-strand	84-85	2	42
β-strand	90-92	3	43
β-strand	103-107	5	42
β-strand	118-121	4	42
β-strand	126-129	4	42
β-strand	169-172	4	42
β-strand	191-197	7	43
β-strand	200-206	7	43
β-strand	223	1	40
β-strand	224-230	7	43
β-strand	237-241	5	42
β-strand	269	1	43
β-strand	271-279	9	41
β-strand	285-290	6	41
α-helix	295-303	9
β-strand	313-319	7	44
α-helix	320-322	3
β-strand	326-328	3	3
α-helix	338-342	5
β-strand	356-358	3	45
β-strand	361-362	2	46
β-strand	376-379	4	45
β-strand	392	1	46
β-strand	393-402	10	45
α-helix	405-410	6
α-helix	417-421	5
β-strand	430-437	8	45
β-strand	452-454	3	47
α-helix	460-462	3
β-strand	492-494	3	47
β-strand	508-516	9	45
β-strand	524-525	2	46
β-strand	538-543	6	3
β-strand	546-554	9	3
α-helix	558-560	3
β-strand	565-567	3	3
β-strand	573-577	5	3
β-strand	584-588	5	3
α-helix	589-591	3
β-strand	592-597	6	44
β-strand	610-612	3	44
α-helix	634-636	3
β-strand	642-645	4	44
β-strand	648-651	4	44
β-strand	654-655	2	48
α-helix	656	1
β-strand	664-667	4	48
β-strand	670-674	5	48
β-strand	692-696	5	48
β-strand	701-703	3	18
β-strand	711-728	18	49
β-strand	733-736	4	50
α-helix	738-742	5
α-helix	747-754	8
α-helix	759-782	24
β-strand	787-790	4	34
α-helix	817-825	9
β-strand	858-861	4	50
α-helix	862-863	2
α-helix	867-883	17
α-helix	887-890	4
α-helix	898-908	11
α-helix	913-917	5
α-helix	920-940	21
α-helix	946-964	19
α-helix	965-967	3
α-helix	977-983	7
α-helix	986-1028	43
α-helix	1029-1033	5
β-strand	1047-1056	10	49
β-strand	1059-1077	19	49
β-strand	1081-1083	3	51
β-strand	1086-1090	5	51
β-strand	1094-1097	4	49
β-strand	1102-1105	4	49
β-strand	1113	1	49
β-strand	1116	1	52
β-strand	1120-1122	3	51
β-strand	1133-1134	2	51
β-strand	1138	1	52
α-helix	1141-1145	5

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-23	22
α-helix	27-49	23

Chain h: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	28-49	22

Chain P: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-24	23
α-helix	27-49	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1146	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
de novo designed binder	D, P, h	protein	79	Drosophila melanogaster	Q9VKJ9 (AlphaFold model)

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

>7ZSS_1 Spike glycoprotein (chains A, B, C)
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELD

Sequence of entity 2 (D, P, h), FASTA

>7ZSS_2 de novo designed binder (chains D, P, h)
ETGASSTNMLEALQQRLQFYHGQVARAALENNSGKARRFGRIVKQYEDAIKLYKAGKPVP
YDELPVPPGFGGSENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	32

Primary citation

De novo design of protein interactions with learned surface fingerprints. Gainza, P., Wehrle, S., Van Hall-Beauvais, A. et al. Nature (2023) 617:176-184. DOI 10.1038/s41586-023-05993-x · 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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