7M53: B6 Fab fragment

B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide. Determined by X-ray diffraction at 1.4 Å resolution. Released 26 May 2021.

Method: X-ray diffraction
Resolution: 1.4 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Mus musculus
Chains: 3
Atoms: 4,155
Mol. weight: 49.62 kDa
Released: 26 May 2021

Explore 7M53 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M53 contains 19 α-helices and 46 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1148-1155	8

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	1
α-helix	9-11	3
β-strand	12-14	3	2
β-strand	20-27	8	1
α-helix	31-33	3
β-strand	35-42	8	2
β-strand	46-53	8	2
β-strand	60-62	3	2
β-strand	70-75	6	1
α-helix	76-78	3
β-strand	80-85	6	1
α-helix	90-92	3
β-strand	94-101	8	2
β-strand	111	1	2
β-strand	115-119	5	2
α-helix	123-124	2
β-strand	125	1	3
α-helix	126-127	2
β-strand	128-132	5	4
β-strand	139-140	2	4
β-strand	143-153	11	4
β-strand	154	1	3
β-strand	159-162	4	5
α-helix	163-165	3
β-strand	167	1	5
β-strand	171-173	3	4
α-helix	174-176	3
β-strand	177-178	2	4
β-strand	184-193	10	4
α-helix	194-196	3
β-strand	203-208	6	5
α-helix	209-211	3
β-strand	213-218	6	5

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	6
β-strand	12-16	5	7
β-strand	21-27	7	6
β-strand	32-33	2	8
β-strand	38-39	2	8
β-strand	41-46	6	7
β-strand	53-57	5	7
β-strand	61-62	2	7
α-helix	63	1
β-strand	70-75	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-98	7	7
β-strand	104-105	2	7
β-strand	109-114	6	7
β-strand	118	1	9
α-helix	119-120	2
β-strand	121-125	5	10
α-helix	126-128	3
α-helix	129-133	5
β-strand	136-146	11	10
β-strand	147	1	9
β-strand	152-157	6	11
β-strand	160-161	2	11
α-helix	162	1
β-strand	166-170	5	10
α-helix	171-174	4
β-strand	180-189	10	10
α-helix	190-193	4
β-strand	198-204	7	11
β-strand	212-217	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein stem helix peptide	A	protein	16	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
B6 antigen-binding (Fab) fragment heavy chain	H	protein	220	Mus musculus
B6 antigen-binding (Fab) fragment light chain	L	protein	219	Mus musculus

Sequence of entity 1 (A), FASTA

>7M53_1 Spike glycoprotein stem helix peptide (chains A)
DSFKEELDKYFKNHTS

Sequence of entity 2 (H), FASTA

>7M53_2 B6 antigen-binding (Fab) fragment heavy chain (chains H)
EVQLQQSGPVLVKPGASVRMSCKASGYTITDYYLNWVKQSHGKSLEWLGVLNPYSGGSLY
SQTFKGKATLTVDRSSSTAYLELNSLTSEDSAVYYCARQLGRGNGLDYWGQGTSVTVSSV
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 3 (L), FASTA

>7M53_3 B6 antigen-binding (Fab) fragment light chain (chains L)
NIMMTQSPSSLAVSAGEKVTMSCKSSQSVLHSSDQKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYFCHQYLSSYTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Structural basis for broad coronavirus neutralization. Sauer, M.M., Tortorici, M.A., Park, Y.J. et al. Nat Struct Mol Biol (2021) 28:478-486. DOI 10.1038/s41594-021-00596-4 · 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
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…
6M1V 1.5 Å, Crystal structure of post fusion core of 2019-nCoV S2 subunit

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