8CWK: Fab arm of antibodies 4G1-C2 and 10G4

Fab arm of antibodies 4G1-C2 and 10G4 bound to CoV-2 receptor binding domain (RBD). Determined by X-ray diffraction at 2.37 Å resolution. Released 24 May 2023.

Method: X-ray diffraction
Resolution: 2.37 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 5
Atoms: 8,339
Mol. weight: 120.46 kDa
Ligands: NAG
Released: 24 May 2023

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

Secondary structure: helices and β-sheets

8CWK contains 47 α-helices and 106 β-strands across 5 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, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	102	1	13
β-strand	105	1	13
β-strand	108-111	4	12
β-strand	115-119	5	12
β-strand	125	1	14
α-helix	126-127	2
β-strand	128-132	5	15
α-helix	133-135	3
β-strand	143-153	11	15
β-strand	154	1	14
β-strand	159-162	4	16
α-helix	163-165	3
β-strand	167	1	16
β-strand	171-173	3	15
α-helix	174-176	3
β-strand	177-178	2	15
β-strand	184-193	10	15
α-helix	194-196	3
β-strand	203-208	6	16
α-helix	209-211	3
β-strand	213-218	6	16

Chain B: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	84-90	7	18
α-helix	96	1
β-strand	97-98	2	18
β-strand	102-106	5	18
β-strand	111	1	19
α-helix	112-113	2
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	20
β-strand	140	1	19
β-strand	145-150	6	21
β-strand	153-154	2	21
β-strand	159-163	5	20
α-helix	164-167	4
β-strand	173-182	10	20
α-helix	183-186	4
β-strand	191-197	7	21
β-strand	205-210	6	21

Chain C: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	334-335	2	22
α-helix	338-342	5
β-strand	349	1	22
α-helix	350-352	3
β-strand	354-358	5	22
β-strand	361-362	2	22
α-helix	366-369	4
β-strand	376-380	5	22
α-helix	384-389	6
β-strand	391-403	13	22
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	22
α-helix	439-442	4
β-strand	448	1	23
β-strand	452-454	3	24
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	25
β-strand	485	1	25
β-strand	488-489	2	25
β-strand	492-494	3	24
β-strand	497	1	23
α-helix	503-505	3
β-strand	507-517	11	22
β-strand	524-525	2	22

Chain H: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	65	1	1
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	103-107	5	2
β-strand	111-115	5	2
α-helix	119-120	2
β-strand	121	1	3
α-helix	122-123	2
β-strand	124-128	5	4
α-helix	132-134	3
β-strand	135-136	2	4
β-strand	139-149	11	4
β-strand	150	1	3
β-strand	155-158	4	5
α-helix	159-161	3
β-strand	163	1	5
β-strand	167-169	3	4
α-helix	170-172	3
β-strand	173-174	2	4
β-strand	180-189	10	4
α-helix	191-193	3
β-strand	199-204	6	5
α-helix	205-207	3
β-strand	209-214	6	5

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-66	5	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-107	6	7
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	144-150	7	10
β-strand	153-154	2	10
α-helix	155	1
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-186	4
β-strand	191-198	8	10
β-strand	205-210	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of Fab arm of antibody 10G4	H	protein	228	Homo sapiens
Light chain of Fab arm of antibody 10G4	L	protein	215	Homo sapiens
Heavy chain of Fab arm of antibody 4G1-C2	A	protein	232	Homo sapiens
Light chain of Fab arm of antibody 4G1-C2	B	protein	215	Homo sapiens	Q6GMX0 (AlphaFold model)
Spike protein S1	C	protein	204	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>8CWK_1 Heavy chain of Fab arm of antibody 10G4 (chains H)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVIWYDGSDKYY
ADSVKGRFTISRDNSKNTLYLQINSLRAEDTAMYYCAREATAGFDYWGQGNLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Sequence of entity 2 (L), FASTA

>8CWK_2 Light chain of Fab arm of antibody 10G4 (chains L)
NIQMTQSPSAMSASVGDRVTITCRARQDISSYLAWFQQKPGKVPKHLIYAASTLLSGVPS
RFSGSGSGTEFTLTISSLQPEDFATYYCLQHNSYPYTFGQGTKLEINRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Sequence of entity 3 (A), FASTA

>8CWK_3 Heavy chain of Fab arm of antibody 4G1-C2 (chains A)
EVQLLESGGGLVQPGGSLRLSCAASGFRFDYEDMGWVRQAPGKGLEWVSSIDSHGASTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKYSHSVSYGPFDYWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Sequence of entity 4 (B), FASTA

>8CWK_4 Light chain of Fab arm of antibody 4G1-C2 (chains B)
DIQMTQSPSSLSASVGDRVTITCRASQYIYDDLNWYQQKPGKAPKLLIYSASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQAWPYPLTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Sequence of entity 5 (C), FASTA

>8CWK_5 Spike protein S1 (chains C)
TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCF
TNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYL
YRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVV
LSFELLHAPATVCGPKGSHHHHHH

Ligands and cofactors

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

Water and common crystallization additives (GOL) are not listed.

Primary citation

Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies. Mazigi, O., Langley, D.B., Henry, J.Y. et al. Proc Natl Acad Sci U S A (2025) 122:e2417544121-e2417544121. DOI 10.1073/pnas.2417544121 · PubMed

Other PDB entries of the same protein (UniProt Q6GMX0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UCF 1.29 Å, N123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusion peptide residue…
6UCE 1.38 Å, N123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusion peptide residue…
2D7T 1.7 Å, Crystal structure of human anti polyhydroxybutyrate antibody Fv
6UBI 1.9 Å, N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
3BN9 2.17 Å, Crystal Structure of MT-SP1 in complex with Fab Inhibitor E2
5O1R 2.86 Å, human Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B
5VOB 3.02 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21
1BEY 3.25 Å, Antibody to campath-1H humanized FAB
6B70 3.7 Å, Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy…
5VOC 3.99 Å, Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21 - Low…
6B7Z 6.5 Å, Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11 heavy chain…

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