7EAM: Spike protein S1

immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6. Determined by X-ray diffraction at 1.4 Å resolution. Released 17 Mar 2021.

Method: X-ray diffraction
Resolution: 1.4 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Mus musculus
Chains: 6
Atoms: 11,106
Mol. weight: 149.02 kDa
Ligands: NAG
Released: 17 Mar 2021

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

Secondary structure: helices and β-sheets

7EAM contains 55 α-helices and 124 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.

Chains A and B: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	335	1	1
α-helix	338-342	5
β-strand	349	1	2
α-helix	350-352	3
β-strand	354-358	5	2
β-strand	361-362	2	1
α-helix	366-369	4
β-strand	376-380	5	2
β-strand	391-392	2	1
β-strand	394-403	10	2
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	2
α-helix	439-442	4
β-strand	448	1	3
β-strand	452-454	3	4
α-helix	460-462	3
β-strand	469	1	5
α-helix	471-472	2
β-strand	473-474	2	6
β-strand	485	1	6
β-strand	488-489	2	6
β-strand	492-494	3	4
β-strand	497	1	3
α-helix	503-505	3
β-strand	507-516	10	2
β-strand	524-525	2	1

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	23
β-strand	10-12	3	24
β-strand	18-25	8	23
β-strand	27	1	21
α-helix	29-31	3
β-strand	34-39	6	24
β-strand	45-52	8	24
β-strand	57-60	4	24
α-helix	62-64	3
β-strand	65	1	23
β-strand	68-73	6	23
α-helix	74-76	3
β-strand	78-83	6	23
α-helix	88-90	3
β-strand	92-98	7	24
β-strand	110	1	24
β-strand	114-118	5	24
α-helix	121-123	3
β-strand	124	1	25
α-helix	125-126	2
β-strand	127-131	5	26
β-strand	142-152	11	26
β-strand	153	1	25
β-strand	158-161	4	27
α-helix	162-164	3
β-strand	170-172	3	26
α-helix	173-175	3
β-strand	176-178	3	26
β-strand	181-191	11	26
β-strand	201-206	6	27
α-helix	207-209	3
β-strand	211-216	6	27

Chains D and L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-13	4	29
β-strand	19-25	7	28
β-strand	33-38	6	29
β-strand	45-49	5	29
β-strand	53-54	2	29
α-helix	55	1
β-strand	62-67	6	28
β-strand	70-75	6	28
α-helix	80-82	3
β-strand	84-90	7	29
α-helix	98	1
β-strand	99	1	29
α-helix	100	1
β-strand	103-107	5	29
β-strand	112	1	30
α-helix	113-114	2
β-strand	115-119	5	31
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	31
β-strand	141	1	30
β-strand	146-151	6	32
β-strand	154-156	3	32
β-strand	160-164	5	31
α-helix	165-168	4
β-strand	174-183	10	31
α-helix	184-187	4
β-strand	192-198	7	32
α-helix	205	1
β-strand	206-211	6	32

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	18-25	8	7
β-strand	27	1	5
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-52	8	8
β-strand	57-60	4	8
α-helix	62-64	3
β-strand	65	1	7
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-98	7	8
β-strand	109-110	2	8
β-strand	114-118	5	8
α-helix	121-123	3
β-strand	124	1	9
α-helix	125-126	2
β-strand	127-131	5	10
β-strand	142-152	11	10
β-strand	153	1	9
β-strand	158-161	4	11
α-helix	162-164	3
β-strand	170-172	3	10
α-helix	173-175	3
β-strand	176-178	3	10
β-strand	181-191	11	10
β-strand	201-206	6	11
α-helix	207-209	3
β-strand	211-216	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	A, B	protein	233	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
the heavy chain of Fab fragment of antibody 7D6	C, H	protein	220	Mus musculus
the light chain of Fab fragment of antibody 7D6	D, L	protein	214	Mus musculus

Sequence of entity 1 (A, B), FASTA

>7EAM_1 Spike protein S1 (chains A, B)
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFK
CYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNS
NNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQ
PTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFHHHHHHHHHH

Sequence of entity 2 (C, H), FASTA

>7EAM_2 the heavy chain of Fab fragment of antibody 7D6 (chains C, H)
EVQLQQSGAELVRPGASVKLSCTASGFNIKDTYIHWVKQRPEQGLEWIGRIDPGDGDTEY
DPSFQGKATITADTSSNTAYLELSSLTSEDTAVYYCTRFYDYVDYGMDYWGQGTSVTVSS
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIEPR

Sequence of entity 3 (D, L), FASTA

>7EAM_3 the light chain of Fab fragment of antibody 7D6 (chains D, L)
DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPS
RFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPPWTFGGGTKLEVKRADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNN

Ligands and cofactors

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

Primary citation

Cross-neutralizing antibodies bind a SARS-CoV-2 cryptic site and resist circulating variants. Li, T., Xue, W., Zheng, Q. et al. Nat Commun (2021) 12:5652. DOI 10.1038/s41467-021-25997-3

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
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…
6M1V 1.5 Å, Crystal structure of post fusion core of 2019-nCoV S2 subunit

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