8JYR: Anti-HER2 antibody H2Mab-119

Crystal structure of anti-HER2 antibody H2Mab-119 in complex with HER2 domain I. Determined by X-ray diffraction at 1.69 Å resolution. Released 13 Mar 2024.

Method: X-ray diffraction
Resolution: 1.69 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 5,232
Mol. weight: 70.77 kDa
Ligands: NAG
Released: 13 Mar 2024

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

Secondary structure: helices and β-sheets

8JYR contains 26 α-helices and 62 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 A: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	1
β-strand	29	1	2
α-helix	34-36	3
α-helix	39-50	12
β-strand	55-57	3	1
β-strand	59	1	2
β-strand	60-63	4	3
α-helix	72-74	3
β-strand	79-80	2	1
β-strand	84-87	4	3
β-strand	101-102	2	1
β-strand	108	1	3
β-strand	112-117	6	3
β-strand	147-148	2	1
β-strand	152-156	5	3
α-helix	164-166	3
α-helix	169-171	3
β-strand	173	1	1
β-strand	182-184	3	3
α-helix	191-196	6
α-helix	200-202	3
β-strand	204	1	4
α-helix	209-211	3
β-strand	212	1	4

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
β-strand	10-12	3	3
β-strand	18-25	8	5
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	64	1	5
β-strand	67-72	6	5
α-helix	73-75	3
β-strand	77-82	6	5
α-helix	84-86	3
β-strand	88-96	9	3
β-strand	100B-103	5	3
β-strand	107-111	5	3
α-helix	114-116	3
β-strand	117	1	6
α-helix	118-119	2
β-strand	120-124	5	7
β-strand	135-145	11	7
β-strand	146	1	6
β-strand	151-154	4	8
α-helix	155-157	3
β-strand	159	1	8
β-strand	163-165	3	7
α-helix	166-168	3
β-strand	169-171	3	7
β-strand	174-184	11	7
α-helix	185-187	3
β-strand	194-199	6	8
α-helix	200-202	3
β-strand	204-209	6	8

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	9
β-strand	10-14	5	10
β-strand	19-25	7	9
β-strand	30-30A	2	11
β-strand	30D-31	2	11
β-strand	33-38	6	10
β-strand	45-49	5	10
β-strand	53-54	2	10
α-helix	55	1
β-strand	62-67	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	84-90	7	10
β-strand	97-98	2	10
β-strand	102-107	6	10
β-strand	111	1	12
β-strand	114-118	5	13
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	13
β-strand	140	1	12
β-strand	145-150	6	14
β-strand	153-155	3	14
β-strand	159-163	5	13
α-helix	164-167	4
β-strand	173-182	10	13
α-helix	183-186	4
β-strand	191-197	7	14
α-helix	204	1
β-strand	205-210	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor tyrosine-protein kinase erbB-2	A	protein	202	Homo sapiens	P04626 (AlphaFold model)
H2Mab-119 VH-CH1	H	protein	222	Mus musculus
H2Mab-119 light chain	L	protein	218	Mus musculus

Sequence of entity 1 (A), FASTA

>8JYR_1 Receptor tyrosine-protein kinase erbB-2 (chains A)
TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQG
YVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQL
RSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGS
RCWGESSEDCQSLTASHHHHHH

Sequence of entity 2 (H), FASTA

>8JYR_2 H2Mab-119 VH-CH1 (chains H)
EIQLQQSGPELVKPGASVKVSCKASGYAFTSYNMYWVKQSHGKSLEWIGYIDPKHGGTSY
NQKFKGKATMTVDKSSNTANMHLNSLTSEDSAVYYCARMNYGSGYAMDYWGQGTSVTVSS
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (L), FASTA

>8JYR_3 H2Mab-119 light chain (chains L)
NIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFMHWYQQKPGQPPKLLIFLASNLES
GVPPRFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDLRTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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…
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
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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