8JYQ: Cancer-specific anti-HER2 antibody H2Mab-214

Crystal structure of cancer-specific anti-HER2 antibody H2Mab-214 in complex with epitope peptide. Determined by X-ray diffraction at 1.75 Å resolution. Released 13 Mar 2024.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 5,592
Mol. weight: 79.47 kDa
Released: 13 Mar 2024

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

Secondary structure: helices and β-sheets

8JYQ contains 21 α-helices and 54 β-strands across 6 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: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
α-helix	17	1
β-strand	18-25	8	1
β-strand	32-40	9	3
β-strand	46-52	7	3
β-strand	57-59	3	3
α-helix	64-66	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-96	9	3
β-strand	98	1	4
β-strand	100C-103	4	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	117-122	6
α-helix	125-160	36

Chain B: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-7	4	5
β-strand	10-13	4	3
β-strand	19-25	7	5
β-strand	30	1	6
β-strand	31	1	6
β-strand	33-38	6	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	5
β-strand	70-75	6	5
α-helix	80-82	3
β-strand	84-90	7	3
α-helix	96	1
β-strand	97-98	2	3
β-strand	102-106	5	3
α-helix	120-158	39

Chains C and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	613	1	4

Chain D: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
α-helix	17	1
β-strand	18-25	8	7
β-strand	32-39	8	9
β-strand	46-52	7	9
β-strand	57-59	3	9
α-helix	61-66	6
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	9
β-strand	98	1	10
β-strand	100C-103	4	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	117-120	4
α-helix	125-162	38

Chain E: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	9
β-strand	19-25	7	11
β-strand	30-30A	2	12
β-strand	30D-31	2	12
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-90	6	9
α-helix	96	1
β-strand	97-98	2	9
β-strand	102-106	5	9
α-helix	113-117	5
α-helix	120-157	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H2CasMab-1 VH(S112C),SARAH	A, D	protein	174	Mus musculus, Homo sapiens
H2CasMab-1 VL,SARAH(S37C)	B, E	protein	170	Mus musculus, Homo sapiens
H2CasMab-1 epitope peptide	C, F	protein	8	Homo sapiens	P04626 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8JYQ_1 H2CasMab-1 VH(S112C),SARAH (chains A, D)
GRQVTLKESGPGILQPSQTLSLTCSFSGFSLSTSGMGVSWIRQPSGKGLEWLAHIFWDDD
KRYNPSLKSRLTISKDTSRNKVFLKITSVDTADTATYYCARRVVATDWYFDVWGAGTTVT
VCSGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQSKRQPILDAIEAK

Sequence of entity 2 (B, E), FASTA

>8JYQ_2 H2CasMab-1 VL,SARAH(S37C) (chains B, E)
GRDIVLTQSPASLAVSLGQRATISCRASESVEYYGTTLMQWYQQKPGQPPKLLIYAASKV
ESGVPARFSGSGSGTDFSLNIHPVEEDDVAMYFCQQSRKVPLTFGAGTKLELKRGSDYEF
LKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQCKRQPILDAIEAKGTLLG

Sequence of entity 3 (C, F), FASTA

>8JYQ_3 H2CasMab-1 epitope peptide (chains C, F)
MPIWKFPD

Primary citation

Locally misfolded HER2 expressed on cancer cells is a promising target for development of cancer-specific antibodies. Arimori, T., Mihara, E., Suzuki, H. et al. Structure (2024) 32:536-549.e5. DOI 10.1016/j.str.2024.02.007 · 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…
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
9IUT 2.09 Å, Crystal structure of cancer-specific anti-HER2 antibody H2Mab-250 in complex with…
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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