8DTR: SARS-CoV-2 spike stem helix peptide

Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV30-14. Determined by X-ray diffraction at 1.5 Å resolution. Released 23 Nov 2022.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 6
Atoms: 7,812
Mol. weight: 98.49 kDa
Released: 23 Nov 2022

Explore 8DTR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DTR contains 35 α-helices and 85 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-24	7	1
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-71	4	1
β-strand	79-83	5	1
α-helix	88-90	3
β-strand	92-99	8	2
α-helix	100	1
β-strand	105-108	4	2
β-strand	112-116	5	2
β-strand	122	1	3
α-helix	123-124	2
β-strand	125-129	5	4
β-strand	140-150	11	4
β-strand	151	1	3
β-strand	156-159	4	5
α-helix	160-162	3
β-strand	164	1	5
β-strand	168-170	3	4
α-helix	171-173	3
β-strand	174-175	2	4
β-strand	181-190	10	4
α-helix	191-195	5
β-strand	198	1	6
β-strand	199-205	7	5
α-helix	206-208	3
β-strand	210-216	7	5

Chain B: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-29	11	7
α-helix	31-33	3
β-strand	34-39	6	8
β-strand	46-50	5	8
β-strand	55	1	8
α-helix	56	1
β-strand	63-76	14	7
α-helix	81-83	3
β-strand	85-94	10	8
β-strand	97-101	5	8
β-strand	105-109	5	8
β-strand	114	1	9
α-helix	115-116	2
β-strand	117-121	5	10
α-helix	122-124	3
α-helix	125-129	5
β-strand	132-142	11	10
β-strand	143	1	9
β-strand	148-153	6	11
β-strand	156-157	2	11
α-helix	158	1
β-strand	162-166	5	10
α-helix	167-170	4
β-strand	176-185	10	10
α-helix	186-190	5
β-strand	194-200	7	11
β-strand	208-213	6	11

Chain E: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
α-helix	7-9	3
β-strand	10-12	3	12
β-strand	18-26	9	6
β-strand	34-39	6	12
β-strand	46-51	6	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-72	5	6
β-strand	79-83	5	6
α-helix	88-90	3
β-strand	92-99	8	12
α-helix	100	1
β-strand	105-108	4	12
β-strand	112-116	5	12
β-strand	122	1	13
β-strand	125-129	5	14
β-strand	140-150	11	14
β-strand	151	1	13
β-strand	156-159	4	15
α-helix	160-162	3
β-strand	164	1	15
β-strand	168-170	3	14
α-helix	171-173	3
β-strand	174-175	2	14
β-strand	181-190	10	14
α-helix	191-195	5
β-strand	200-205	6	15
α-helix	206-208	3
β-strand	210-215	6	15

Chain F: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-13	4	17
β-strand	19-29	11	16
α-helix	31-33	3
β-strand	34-39	6	17
β-strand	46-50	5	17
β-strand	55	1	17
β-strand	63-76	14	16
α-helix	81-83	3
β-strand	86-94	9	17
β-strand	97-101	5	17
β-strand	105-109	5	17
β-strand	114	1	18
α-helix	115-116	2
β-strand	117-121	5	19
α-helix	122-124	3
α-helix	125-130	6
β-strand	132-142	11	19
β-strand	143	1	18
β-strand	148-153	6	20
β-strand	156-157	2	20
β-strand	162-166	5	19
α-helix	167-170	4
β-strand	176-185	10	19
α-helix	186-190	5
β-strand	194-200	7	20
β-strand	208-213	6	20

Chains G and J: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1148-1157	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
COV30-14 heavy chain	A, E	protein	221	Homo sapiens
COV30-14 light chain	B, F	protein	217	Homo sapiens
Spike protein S2' stem helix peptide	G, J	protein	15	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>8DTR_1 COV30-14 heavy chain (chains A, E)
QVQLVQSGAEVKKPGASVKVSCQTSGYTFTSYYMHWVRQAPGQGLEWMGLITPSGDDTYY
AQRFQGRVTMTRDTSTSPTYMELSSLTSEDTAVYYCAKMSRAGGFDVWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (B, F), FASTA

>8DTR_2 COV30-14 light chain (chains B, F)
EVVLTQSPGTLSLSPGERATLSCRASQSITGRYLAWYQQKPGQAPRLLMYGESSRVTGIP
DRFSGGGSGTDFTLTISRLEPEDFAVYYCQHFASSPPTYTFGQGTKLEIRRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (G, J), FASTA

>8DTR_3 Spike protein S2' stem helix peptide (chains G, J)
LDSFKEELDKYFKNH

Primary citation

Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses. Dacon, C., Peng, L., Lin, T.H. et al. Cell Host Microbe (2023) 31:97. DOI 10.1016/j.chom.2022.10.010 · 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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