8AXH: Single-chain variable antibody SM3

Crystal structure of a MUC1-like glycopeptide containing the unnatural L-4-hydroxynorvaline in complex with scFv-SM3. Determined by X-ray diffraction at 1.85 Å resolution. Released 9 Aug 2023.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 2,004
Mol. weight: 27.02 kDa
Ligands: A2G
Released: 9 Aug 2023

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

Secondary structure: helices and β-sheets

8AXH contains 7 α-helices and 23 β-strands across 1 chain. 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 H: 7 helices, 23 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	34-40	7	2
β-strand	44-51	8	2
α-helix	52B-53	3
β-strand	57-59	3	2
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-94	7	2
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	1005-1007	3	3
β-strand	1010-1013	4	4
β-strand	1018-1025	8	3
β-strand	1027A	1	3
α-helix	1029-1031	3
β-strand	1034-1039	6	4
β-strand	1043-1049	7	4
β-strand	1053-1054	2	4
α-helix	1055	1
β-strand	1062-1067	6	3
β-strand	1070-1076	7	3
α-helix	1080-1082	3
β-strand	1084-1092	9	4
β-strand	1095-1098	4	4
β-strand	1102-1106	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Single-chain variable antibody (scFv) SM3	H	protein	244	Mus musculus
Mucin-1 subunit alpha	A	protein	7	Homo sapiens	P15941 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>8AXH_1 Single-chain variable antibody (scFv) SM3 (chains H)
QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYAT
HYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSSSSG
GGGSGGGGGSSGSSDIVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLF
TGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKL
TVLG

Sequence of entity 2 (A), FASTA

>8AXH_2 Mucin-1 subunit alpha (chains A)
APDXRPX

Ligands and cofactors

ID	Name	Formula	Copies
A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	C8 H15 N O6	1

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

Primary citation

Structure-Guided Approach for the Development of MUC1-Glycopeptide-Based Cancer Vaccines with Predictable Responses. Bermejo, I.A., Guerreiro, A., Eguskiza, A. et al. JACS Au (2024) 4:150-163. DOI 10.1021/jacsau.3c00587 · PubMed

Other PDB entries of the same protein (UniProt P15941 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BSC 1.3 Å, Crystal structure of the Mucin-1 SEA domain
7V64 1.56 Å, Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoT)
6BSB 1.6 Å, Crystal structure of the Mucin-1 SEA domain, L1105M mutant, Selenium-derivative
6FZQ 1.7 Å, Crystal structure of scFv-SM3 in complex with compound 3
8S6K 1.75 Å, Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide
6KX1 1.77 Å, Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide
6FZR 1.8 Å, Crystal structure of scFv-SM3 in complex with compound 2
8S6T 1.85 Å, Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide
1SM3 1.95 Å, Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope
8S6V 1.95 Å, Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide
5T6P 1.97 Å, Crystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide
6TGG 2.0 Å, scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar

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