7B0B: Fab HbnC3t1p1_C6

Fab HbnC3t1p1_C6 bound to SARS-CoV-2 RBD. Determined by X-ray diffraction at 2.98 Å resolution. Released 1 Dec 2021.

Method: X-ray diffraction
Resolution: 2.98 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 4,858
Mol. weight: 74.45 kDa
Released: 1 Dec 2021

Explore 7B0B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B0B contains 25 α-helices and 62 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: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	334	1
β-strand	335	1	12
α-helix	336	1
α-helix	338-342	5
β-strand	349	1	13
β-strand	354-358	5	13
β-strand	361-362	2	12
α-helix	366-369	4
β-strand	376-380	5	13
α-helix	386-389	4
β-strand	391-392	2	12
β-strand	394-403	10	13
α-helix	404-409	6
α-helix	417-421	5
β-strand	431-437	7	13
α-helix	439-442	4
β-strand	448	1	14
β-strand	452-454	3	15
α-helix	460-462	3
α-helix	471-472	2
β-strand	473-474	2	16
β-strand	485	1	16
β-strand	488-489	2	16
β-strand	492-494	3	15
β-strand	497	1	14
α-helix	503-505	3
β-strand	507-516	10	13
β-strand	524-525	2	12

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	33-39	7	7
β-strand	45-52	8	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-98	7	7
β-strand	101	1	8
β-strand	106	1	8
β-strand	112-113	2	7
β-strand	117-121	5	7
α-helix	124-126	3
β-strand	127	1	9
β-strand	130-134	5	10
α-helix	135-137	3
β-strand	145-155	11	10
β-strand	156	1	9
β-strand	161-164	4	11
β-strand	173-175	3	10
α-helix	176-178	3
β-strand	179-180	2	10
β-strand	186-195	10	10
α-helix	196-198	3
β-strand	204-210	7	11
β-strand	215-221	7	11

Chain L: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	34-39	6	2
α-helix	44-45	2
β-strand	46-50	5	2
β-strand	54-55	2	2
α-helix	56	1
β-strand	63-68	6	1
β-strand	71-76	6	1
α-helix	81-83	3
β-strand	86-91	6	2
β-strand	99	1	2
β-strand	100	1	1
β-strand	103-107	5	2
β-strand	112	1	3
β-strand	117-119	3	4
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	4
β-strand	141	1	3
β-strand	146-151	6	5
β-strand	154-156	3	5
β-strand	160-164	5	4
α-helix	165-168	4
β-strand	174-183	10	4
α-helix	184-187	4
β-strand	192-198	7	5
β-strand	206-211	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IGK@ protein	L	protein	215	Homo sapiens	Q6PIL8 (AlphaFold model)
Fab heavy chain	H	protein	230	Homo sapiens
Surface glycoprotein	F	protein	229	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>7B0B_1 IGK@ protein (chains L)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRVEPEDFAVYYCQQYGSSPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>7B0B_2 Fab heavy chain (chains H)
QMQLVQSGPEVKKPGTSVKVSCKASGFTFTSSAVQWVRQARGQRLEWIGWIVVGSGNTNY
AQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPHCSSTICYDGFDIWGQGTMVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Sequence of entity 3 (F), FASTA

>7B0B_3 Surface glycoprotein (chains F)
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFK
CYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNS
NNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQ
PTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFHHHHHH

Primary citation

Somatic hypermutation introduces bystander mutations that prepare SARS-CoV-2 antibodies for emerging variants. Korenkov, M., Zehner, M., Cohen-Dvashi, H. et al. Immunity (2023) 56:2803-2815.e6. DOI 10.1016/j.immuni.2023.11.004 · PubMed

Other PDB entries of the same protein (UniProt Q6PIL8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6E56 2.0 Å, Human antibody H2214 in complex with influenza hemagglutinin A/Aichi/2/1968 (X-31) (H3N2)
6UDJ 2.5 Å, HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074
6BKB 2.8 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to…
3HI1 2.9 Å, Structure of HIV-1 gp120 (core with V3) in Complex with CD4-Binding-Site Antibody F105
6V8X 3.0 Å, VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
4OQT 3.23 Å, LINGO-1/Li81 Fab complex
6BKD 3.25 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to…
5UG0 3.4 Å, Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
5W1K 3.99 Å, JUNV GP1 CR1-10 Fab CR1-28 Fab complex

Browse structure collections

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