8D36: SARS-CoV-2 fusion peptide

Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody COV44-62. Determined by X-ray diffraction at 1.45 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 1.45 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 3,877
Mol. weight: 48.69 kDa
Released: 27 Jul 2022

Explore 8D36 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D36 contains 18 α-helices and 47 β-strands across 3 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 F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	815-822	8

Chain H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	17-25	9	1
α-helix	29-31	3
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	68-73	6	1
α-helix	74-76	3
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	113-114	2	2
β-strand	118-122	5	2
α-helix	126-127	2
β-strand	128	1	3
α-helix	129-130	2
β-strand	131-135	5	4
β-strand	148-158	11	4
β-strand	159	1	3
β-strand	164-167	4	5
α-helix	168-170	3
β-strand	172	1	5
β-strand	176-178	3	4
α-helix	179-181	3
β-strand	182-183	2	4
β-strand	189-198	10	4
α-helix	199-201	3
β-strand	208-213	6	5
α-helix	214-216	3
β-strand	218-223	6	5

Chain L: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	6
β-strand	5	1	7
β-strand	9-12	4	8
β-strand	18-23	6	7
β-strand	35-40	6	8
β-strand	47-50	4	8
β-strand	51	1	9
β-strand	55	1	9
β-strand	64-69	6	7
β-strand	72-77	6	7
α-helix	82-84	3
β-strand	86-94	9	8
β-strand	98-101	4	8
β-strand	102	1	6
β-strand	105-109	5	8
α-helix	112-114	3
β-strand	115	1	10
α-helix	116-117	2
β-strand	118-122	5	11
α-helix	123-125	3
α-helix	126-130	5
β-strand	134-143	10	11
β-strand	144	1	10
β-strand	149-154	6	12
β-strand	157-159	3	12
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-184	9	11
α-helix	186-191	6
β-strand	195-201	7	12
β-strand	204-210	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neutralizing antibody COV44-62 heavy chain	H	protein	227	Homo sapiens
Neutralizing antibody COV44-62 light chain	L	protein	216	Homo sapiens
Spike protein S2 fusion peptide	F	protein	15	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>8D36_1 Neutralizing antibody COV44-62 heavy chain (chains H)
QMQLMQSGAEVKKPGASVTVSCKASGDTFSDYRIHWVRQAPGQGLEWMGRMNPKSGDTNF
AQKFQGRVTMTRDMSINTAYMTLSGLTFDDTALYYCASLLIVGGFDPLDDFEVWGQGTMV
TISSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (L), FASTA

>8D36_2 Neutralizing antibody COV44-62 light chain (chains L)
QSALTQPPSASGSPGQSVTISCSGTSSDVGGYNFVSWYQHHPGKAPKILIYEVTKRPSGV
PDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYGGTNNLLFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (F), FASTA

>8D36_3 Spike protein S2 fusion peptide (chains F)
PSKRSFIEDLLFNKV

Primary citation

Broadly neutralizing antibodies target the coronavirus fusion peptide. Dacon, C., Tucker, C., Peng, L. et al. Science (2022) 377:728-735. DOI 10.1126/science.abq3773 · 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
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…
6M1V 1.5 Å, Crystal structure of post fusion core of 2019-nCoV S2 subunit

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