7SD5: Spike protein S1

Crystallographic structure of neutralizing antibody 10-40 in complex with SARS-CoV-2 spike receptor binding domain. Determined by X-ray diffraction at 1.53 Å resolution. Released 27 Apr 2022.

Method: X-ray diffraction
Resolution: 1.53 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 3
Atoms: 5,628
Mol. weight: 75.78 kDa
Released: 27 Apr 2022

Explore 7SD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SD5 contains 27 α-helices and 64 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 A: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	338-342	5
β-strand	349	1	1
α-helix	350-352	3
β-strand	354-358	5	1
β-strand	361-362	2	2
α-helix	366-369	4
β-strand	376-380	5	1
α-helix	384-389	6
β-strand	391-392	2	2
β-strand	394-403	10	1
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	1
α-helix	439-442	4
β-strand	448	1	3
β-strand	452-454	3	4
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	5
β-strand	485	1	5
β-strand	488-489	2	5
β-strand	492-494	3	4
β-strand	497	1	3
α-helix	503-505	3
β-strand	507-516	10	1
β-strand	524-525	2	2

Chain H: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
β-strand	35A-39	6	8
β-strand	46-51	6	8
β-strand	57-59	3	8
α-helix	64-66	3
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	8
α-helix	96-98	3
β-strand	99-100	2	1
β-strand	100F-100G	2	1
β-strand	100L-103	4	8
β-strand	107-109	3	8
β-strand	110-111	2	7
α-helix	115-116	2
β-strand	117	1	9
β-strand	120-124	5	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-188	3
β-strand	195-200	6	11
α-helix	201-203	3
β-strand	205-210	6	11

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	12
β-strand	9-12	4	13
β-strand	18-24	7	12
α-helix	28-30	3
β-strand	34-38	5	13
β-strand	45-48	4	13
β-strand	49	1	14
β-strand	53	1	14
β-strand	62-66A	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-92	9	13
β-strand	95-98	4	13
β-strand	102-106	5	13
α-helix	109-111	3
β-strand	112	1	15
α-helix	113-114	2
β-strand	115-119	5	16
α-helix	123-127	5
β-strand	131-140	10	16
β-strand	141	1	15
β-strand	146-151	6	17
β-strand	154-155	2	17
α-helix	156	1
β-strand	160-162	3	16
α-helix	163-165	3
β-strand	166-167	2	16
β-strand	173-181	9	16
α-helix	183-188	6
β-strand	192-198	7	17
β-strand	201-207	7	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	A	protein	239	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
10-40 Heavy chain	H	protein	236	Homo sapiens
10-40 Light chain	L	protein	216	Homo sapiens

Sequence of entity 1 (A), FASTA

>7SD5_1 Spike protein S1 (chains A)
APRRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFS
TFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIA
WNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSY
GFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKGSLEVLFQGPGHHHHHH

Sequence of entity 2 (H), FASTA

>7SD5_2 10-40 Heavy chain (chains H)
QLQLQESGPGLVKPSETLSLTCTVSGGSISSSNFYWGWIRQPPGKGLEWIASITYSGRTF
YNPSLKSRVAISVDTSKNQFSLKLSSVTAADTAVYYCARTFPSYYDRSGYHYLNYGMDVW
GQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKT

Sequence of entity 3 (L), FASTA

>7SD5_3 10-40 Light chain (chains L)
NFMLTQPHSMSESPGKTVTISCTRSSGSIASNYVQWYQQRPGSSPTTVIYEDNQRPSGVP
DRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSSWVFGGGTKLTVLGQPKANPTVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses. Liu, L., Iketani, S., Guo, Y. et al. Sci Transl Med (2022) 14:eabn6859-eabn6859. DOI 10.1126/scitranslmed.abn6859 · 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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