9IUT: Cancer-specific anti-HER2 antibody H2Mab-250

Crystal structure of cancer-specific anti-HER2 antibody H2Mab-250 in complex with epitope peptide. Determined by X-ray diffraction at 2.09 Å resolution. Released 4 Jun 2025.

Method: X-ray diffraction
Resolution: 2.09 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 5,671
Mol. weight: 77.96 kDa
Released: 4 Jun 2025

Explore 9IUT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IUT contains 24 α-helices and 50 β-strands across 4 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: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57-58	2	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-93	6	3
β-strand	103	1	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	118-122	5
α-helix	125-161	37

Chain B: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-7	4	4
β-strand	10-13	4	5
β-strand	19-25	7	4
β-strand	30	1	6
β-strand	31	1	6
β-strand	33-38	6	5
β-strand	45-49	5	5
β-strand	53-54	2	5
α-helix	55	1
β-strand	62-67	6	4
β-strand	70-75	6	4
α-helix	80-82	3
β-strand	84-90	7	5
α-helix	97	1
β-strand	98	1	5
α-helix	99	1
β-strand	102-106	5	5
α-helix	115-117	3
α-helix	120-157	38

Chain D: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	17-25	9	7
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	57-58	2	9
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82A	7	7
α-helix	84-86	3
β-strand	88-93	6	9
β-strand	103	1	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	112-113	2
α-helix	118-122	5
α-helix	125-161	37

Chain E: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-12	3	11
β-strand	19-25	7	10
β-strand	30	1	12
β-strand	31	1	12
β-strand	33-38	6	11
β-strand	44-49	6	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	84-90	7	11
α-helix	97	1
β-strand	98	1	11
α-helix	99	1
β-strand	102-105	4	11
α-helix	113-117	5
α-helix	120-128	9
α-helix	130-158	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H2Mab-250 VH(S112C)-SARAH	A, D	protein	169	Mus musculus
H2Mab-250 VL-SARAH(S37C)	B, E	protein	171	Mus musculus
H2Mab-250 epitope peptide	C, F	protein	8	Homo sapiens	P04626 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9IUT_1 H2Mab-250 VH(S112C)-SARAH (chains A, D)
GREVQLVESGGGLVQPGGSLKLSCAASGFTFSNYGMSWVRQTPDRRLELVATINNNGGGT
YYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTSPGLLWDAWGAGTTVTVCSGS
DYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQSKRQPILDAIEAK

Sequence of entity 2 (B, E), FASTA

>9IUT_2 H2Mab-250 VL-SARAH(S37C) (chains B, E)
GRDVVMTQTPLTLSVSIGQPASISCKSSQSLLDSDGRTYLNWLLQRPGQSPKRLIYLVSK
LDSGAPDRFTGSGSGTDFTLKISRVEAEDLGVYYCWQGTHFPQTFGGGTKLEIKRGSDYE
FLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQCKRQPILDAIEAKGTLLG

Sequence of entity 3 (C, F), FASTA

>9IUT_3 H2Mab-250 epitope peptide (chains C, F)
MPIWKFPD

Primary citation

Preferential tumor targeting of HER2 by iPSC-derived CAR T cells engineered to overcome multiple barriers to solid tumor efficacy. Hosking, M.P., Shirinbak, S., Omilusik, K. et al. Cell Stem Cell (2025) 32:1087-1101.e4. DOI 10.1016/j.stem.2025.05.007 · PubMed

Other PDB entries of the same protein (UniProt P04626 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MFG 1.25 Å, The Structure of ERBIN PDZ domain bound to the Carboxy-terminal tail of the ErbB2 Receptor
8VB5 1.48 Å, Crystal structure of kinase domain of HER2 Exon 20 insertion mutant in complex with…
8JYR 1.69 Å, Crystal structure of anti-HER2 antibody H2Mab-119 in complex with HER2 domain I
8U8X 1.69 Å, crystal structure of the receptor tyrosine kinase Human HER2 (ERBB2) YVMA mutant kinase…
8JYQ 1.75 Å, Crystal structure of cancer-specific anti-HER2 antibody H2Mab-214 in complex with…
7PCD 1.77 Å, HER2 in complex with a covalent inhibitor
5TQS 1.88 Å, Phospholipase C gamma-1 C-terminal SH2 domain bound to a phosphopeptide derived from the…
1MFL 1.88 Å, The Structure of ERBIN PDZ domain bound to the Carboxy-terminal tail of the ErbB2 Receptor
4GFU 2.0 Å, PTPN18 in complex with HER2-pY1248 phosphor-peptides
6LBX 2.03 Å, Crystal structure of HER2 Domain IV and Rb-H2
5MY6 2.25 Å, Crystal structure of a HER2-Nb complex
3PP0 2.25 Å, Crystal Structure of the Kinase domain of Human HER2 (erbB2).

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