7STR: Fab S24-1063, Light chain

Crystal Structure of Human Fab S24-1063 in the Complex with the N-teminal Domain of Nucleocapsid Protein from SARS CoV-2. Determined by X-ray diffraction at 1.5 Å resolution. Released 10 Aug 2022.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 4,810
Mol. weight: 61.82 kDa
Released: 10 Aug 2022

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

Secondary structure: helices and β-sheets

7STR contains 29 α-helices and 57 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 C: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	11
β-strand	53	1	12
α-helix	54-55	2
β-strand	56-57	2	13
β-strand	58	1	14
α-helix	63-64	2
α-helix	72-74	3
α-helix	80-82	3
β-strand	84-90	7	13
β-strand	93-95	3	15
β-strand	101-103	3	15
α-helix	104-106	3
β-strand	107-112	6	13
α-helix	122	1
β-strand	130-134	5	13
β-strand	149	1	11
α-helix	155-156	2
β-strand	157	1	12
α-helix	158-159	2
α-helix	167-168	2
β-strand	171	1	14

Chain H: 10 helices, 24 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	33-39	7	2
β-strand	46-52	7	2
β-strand	57-59	3	2
α-helix	64-66	3
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	87-89	3
β-strand	91-98	8	2
β-strand	109-112	4	2
β-strand	116-118	3	2
β-strand	119-120	2	7
α-helix	123-125	3
β-strand	126	1	8
α-helix	127-128	2
β-strand	129-133	5	9
α-helix	137-139	3
β-strand	140-141	2	9
β-strand	144-154	11	9
β-strand	155	1	8
β-strand	160-163	4	10
α-helix	164-166	3
β-strand	168	1	10
β-strand	172-174	3	9
α-helix	175-177	3
β-strand	178-179	2	9
β-strand	185-194	10	9
α-helix	195-197	3
β-strand	204-209	6	10
α-helix	210-212	3
β-strand	214-219	6	10

Chain L: 10 helices, 21 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
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	85-91	7	2
α-helix	97	1
β-strand	98-99	2	2
β-strand	103-107	5	2
α-helix	108	1
β-strand	112	1	3
α-helix	113-114	2
β-strand	115-119	5	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	154-155	2	5
α-helix	156	1
β-strand	160-164	5	4
α-helix	165-168	4
β-strand	174-183	10	4
α-helix	184-188	5
β-strand	192-198	7	5
β-strand	206-211	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab S24-1063, Light chain	L	protein	215	Homo sapiens
Fab S24-1063, Heavy chain	H	protein	222	Homo sapiens
Nucleoprotein	C	protein	130	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>7STR_1 Fab S24-1063, Light chain (chains L)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATDIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>7STR_2 Fab S24-1063, Heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTKYN
PSLKSRVTISVDTSKNQFSLKLTSVTAADTAVYYCARIYDSSGYYHPVFDYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP

Sequence of entity 3 (C), FASTA

>7STR_3 Nucleoprotein (chains C)
SNMNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKD
LSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQ
GTTLPKGFYA

Primary citation

Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. Kim, Y., Maltseva, N., Tesar, C. et al. iScience (2024) 27:108976-108976. DOI 10.1016/j.isci.2024.108976 · PubMed

Other PDB entries of the same protein (UniProt P0DTC9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7LUZ 1.1 Å, GQTVTK segment from the Nucleoprotein of SARS-CoV-2, residues 243-248
7LTU 1.12 Å, Aalall segment from the nucleoprotein of SARS-CoV-2, residues 217-222, crystal form 1
7VBF 1.3 Å, 1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization…
9F2H 1.3 Å, Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with riluzole
7LV2 1.3 Å, GSQASS segment from the Nucleoprotein of SARS-CoV-2, residues 179-184
7LUX 1.3 Å, AALALL segment from the Nucleoprotein of SARS-CoV-2, residues 217-222, crystal form 2
7KGQ 1.34 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N222-230
6ZCO 1.36 Å, Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from…
7KGP 1.4 Å, Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N316-324
9IN1 1.4 Å, Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2
6WZO 1.42 Å, Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P1 form
7N0R 1.42 Å, Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody…

Browse structure collections

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