7N3D: S24-1564 Fab heavy chain

Crystal Structure of Human Fab S24-1564 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2. Determined by X-ray diffraction at 1.53 Å resolution. Released 7 Jul 2021.

Method: X-ray diffraction
Resolution: 1.53 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 4,910
Mol. weight: 62.32 kDa
Released: 7 Jul 2021

Explore 7N3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N3D contains 25 α-helices and 55 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: 6 helices, 9 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
α-helix	72-74	3
α-helix	80-82	3
β-strand	84-89	6	13
β-strand	107-112	6	13
α-helix	121-122	2
β-strand	130-134	5	13
β-strand	139	1	2
β-strand	149	1	11
α-helix	155-156	2
β-strand	157	1	12
α-helix	158-159	2

Chain H: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
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	1
β-strand	77-82	6	1
α-helix	87-89	3
β-strand	91-101	11	2
β-strand	104-112	9	2
β-strand	116-120	5	2
α-helix	124-125	2
β-strand	126	1	3
α-helix	127-128	2
β-strand	129-133	5	4
α-helix	137-139	3
β-strand	140-141	2	4
β-strand	144-154	11	4
β-strand	155	1	3
β-strand	160-163	4	5
α-helix	164-166	3
β-strand	168	1	5
β-strand	172-174	3	4
α-helix	175-177	3
β-strand	178-179	2	4
β-strand	185-194	10	4
α-helix	195-197	3
β-strand	198	1	6
β-strand	201	1	6
β-strand	204-209	6	5
α-helix	210-212	3
β-strand	214-219	6	5

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-14	5	2
β-strand	19-25	7	7
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-65	4	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
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	145-150	6	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	191-197	7	10
β-strand	205-210	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S24-1564 Fab heavy chain	H	protein	225	Homo sapiens
S24-1564 Fab light chain	L	protein	214	Homo sapiens
Nucleoprotein	C	protein	130	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7N3D_1 S24-1564  Fab heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYVYYSGNTKYN
PSLKSRVTISVDTSKNQFSLKLGSVTAADTAVYYCARHSRIEVAGTLDFDYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (L), FASTA

>7N3D_2 S24-1564 Fab light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSIRSYLNWYQQKRGKAPKLLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>7N3D_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…

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