8VQD: HER2 S310F

HER2 S310F in complex with TL1 Fab. Determined by electron microscopy at 2.61 Å resolution. Released 9 Oct 2024.

Method: Electron microscopy
Resolution: 2.61 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,686
Mol. weight: 150.54 kDa
Released: 9 Oct 2024

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

Secondary structure: helices and β-sheets

8VQD contains 28 α-helices and 85 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: 21 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	1
α-helix	34-36	3
α-helix	39-41	3
α-helix	42-50	9
β-strand	55-57	3	1
β-strand	60-63	4	2
α-helix	72-74	3
β-strand	79-80	2	1
β-strand	84-87	4	2
β-strand	93	1	3
β-strand	101-102	2	1
β-strand	108	1	2
β-strand	112-117	6	2
β-strand	139	1	3
β-strand	147-148	2	1
β-strand	152-156	5	2
β-strand	162	1	3
α-helix	169-172	4
β-strand	173	1	1
α-helix	175-177	3
β-strand	182-184	3	2
α-helix	193-196	4
β-strand	204	1	4
α-helix	209-211	3
β-strand	212	1	4
α-helix	213-215	3
β-strand	227	1	5
β-strand	235	1	5
α-helix	236-237	2
β-strand	240-244	5	6
β-strand	252-255	4	6
β-strand	258-260	3	7
β-strand	263-265	3	7
α-helix	268-270	3
β-strand	272	1	8
β-strand	283	1	8
β-strand	289-291	3	7
β-strand	294-296	3	7
β-strand	304-305	2	9
β-strand	310	1	7
β-strand	311-312	2	9
β-strand	319-323	5	9
β-strand	329-333	5	9
α-helix	338-340	3
β-strand	343	1	10
β-strand	345	1	11
α-helix	348-350	3
α-helix	361-364	4
β-strand	369-370	2	12
β-strand	371	1	10
β-strand	373	1	11
β-strand	374-376	3	13
α-helix	378-382	5
β-strand	384	1	14
β-strand	389	1	14
α-helix	390-392	3
α-helix	395-401	7
β-strand	405-406	2	12
β-strand	410-412	3	13
β-strand	421	1	15
α-helix	423-425	3
β-strand	430-431	2	12
β-strand	437	1	13
β-strand	441-446	6	13
β-strand	452	1	15
β-strand	460-461	2	12
β-strand	465-469	5	13
α-helix	482-485	4
β-strand	486	1	12
β-strand	493-496	4	13
α-helix	501-507	7
β-strand	515	1	16
α-helix	516-518	3
β-strand	520	1	17
β-strand	528	1	17
β-strand	531	1	16
β-strand	534-536	3	18
β-strand	539-541	3	18

Chain B: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	23
β-strand	5-7	3	24
β-strand	10-13	4	25
β-strand	19-24	6	24
α-helix	30-32	3
β-strand	33-38	6	25
β-strand	45-48	4	25
α-helix	53	1
β-strand	54	1	25
α-helix	55	1
β-strand	62-67	6	24
β-strand	70-75	6	24
α-helix	80-82	3
β-strand	85-91	7	25
β-strand	97-99	3	25
β-strand	100	1	23
β-strand	103-107	5	25

Chain C: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	11-12	2	20
β-strand	17-24	8	19
α-helix	27-30	4
β-strand	33-39	7	21
β-strand	45-52	8	21
β-strand	58-60	3	21
β-strand	65	1	19
β-strand	68-73	6	19
β-strand	78-84	7	19
α-helix	88-90	3
β-strand	92-99	8	21
β-strand	102-104	3	22
α-helix	106-108	3
β-strand	110-112	3	22
β-strand	116-119	4	21
β-strand	123-125	3	21
β-strand	126-127	2	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor tyrosine-protein kinase erbB-2/hIgG1 Fc domain fusion	A	protein	894	Homo sapiens	P04626 (AlphaFold model)
Variable Heavy chain of TL1 Fab	C	protein	257	Homo sapiens
Variable Light chain of TL1 Fab	B	protein	215	Homo sapiens

Sequence of entity 1 (A), FASTA

>8VQD_1 Receptor tyrosine-protein kinase erbB-2/hIgG1 Fc domain fusion (chains A)
TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQG
YVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQL
RSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGS
RCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSG
ICELHCPALVTFNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGFCTLVCPLHNQEV
TAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFD
GDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYS
LTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPED
ECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLP
CHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGA
CQPCPINCTHSCVDLDDKGCPAEQRASPLTPGSRSPKSCDKTHTCPPCPAPELLGGPSVF
LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYR
VVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKN
QVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGN
VFSCSVMHEALHNHYTQKSLSLSPGKLEGGGGLNDIFEAQKIEWHESRHHHHHH

Sequence of entity 2 (C), FASTA

>8VQD_2 Variable Heavy chain of TL1 Fab (chains C)
EISEVQLVESGGGLVQPGGSLRLSCAASGFTWSGAYIHWVRQAPGKGLEWVASIYSAGGY
TDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYGTYELKSYGSWESLPAFD
YWGQGTLVTVFNQIKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTG
GGGLNDIFEAQKIEWHE

Sequence of entity 3 (B), FASTA

>8VQD_3 Variable Light chain of TL1 Fab (chains B)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQSEWGGLITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Selective targeting of oncogenic hotspot mutations of the HER2 extracellular domain. Bang, I., Hattori, T., Leloup, N. et al. Nat Chem Biol (2025) 21:706-715. DOI 10.1038/s41589-024-01751-w · 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
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

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