9IPD: Epidermal growth factor receptor

Poly-alanine model for LH-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (middle conformation). Determined by electron microscopy at 3.29 Å resolution. Released 28 May 2025.

Method: Electron microscopy
Resolution: 3.29 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 5,753
Mol. weight: 148.48 kDa
Released: 28 May 2025

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

Secondary structure: helices and β-sheets

9IPD contains 27 α-helices and 123 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: 14 helices, 64 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	1
α-helix	20-31	12
β-strand	36-37	2	1
β-strand	42-46	5	2
β-strand	60-61	2	1
β-strand	65-70	6	2
β-strand	74	1	3
β-strand	82-83	2	4
β-strand	95-98	4	2
β-strand	110	1	3
β-strand	118-119	2	4
β-strand	124-127	4	2
α-helix	140-143	4
β-strand	144	1	4
α-helix	148-150	3
β-strand	153	1	2
β-strand	212	1	5
β-strand	216	1	6
β-strand	224	1	6
β-strand	227	1	5
β-strand	230-231	2	7
β-strand	236-237	2	7
α-helix	240-242	3
β-strand	244-247	4	8
β-strand	252-255	4	8
β-strand	261-263	3	9
β-strand	266-268	3	9
β-strand	276-277	2	10
β-strand	282	1	9
β-strand	283-284	2	10
β-strand	291-295	5	10
β-strand	300-304	5	10
α-helix	305	1
α-helix	309-310	2
β-strand	311	1	11
β-strand	314	1	12
β-strand	339	1	11
β-strand	341	1	13
β-strand	342	1	12
α-helix	349-353	5
β-strand	355	1	14
β-strand	360	1	14
α-helix	361-364	4
α-helix	365-373	9
β-strand	376-377	2	13
β-strand	381-382	2	15
β-strand	392	1	16
α-helix	394-396	3
β-strand	401-402	2	13
β-strand	408	1	15
β-strand	412-417	6	15
β-strand	423	1	16
β-strand	431	1	13
β-strand	432	1	17
β-strand	436-440	5	15
α-helix	453-456	4
β-strand	457	1	17
α-helix	472-477	6
β-strand	491	1	18
β-strand	499	1	18
β-strand	507	1	19
β-strand	510	1	19
β-strand	524-526	3	20
β-strand	531-533	3	20
α-helix	534-535	2
β-strand	538	1	21
β-strand	547	1	22
β-strand	555	1	22
β-strand	558	1	21
β-strand	562-563	2	23
β-strand	566-567	2	23
β-strand	573-576	4	24
β-strand	577	1	8
α-helix	578-580	3
β-strand	582-584	3	24
β-strand	585-587	3	25
β-strand	592	1	23
β-strand	593-595	3	25

Chain B: 8 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	26
β-strand	15-18	4	27
β-strand	24-34	11	26
β-strand	37-42	6	27
β-strand	49-53	5	27
β-strand	57-58	2	27
α-helix	59	1
β-strand	66-79	14	26
α-helix	84-86	3
β-strand	88-94	7	27
α-helix	100	1
β-strand	101-102	2	27
β-strand	106-110	5	27
α-helix	113-115	3
β-strand	119-122	4	28
β-strand	126-128	3	29
β-strand	134-141	8	28
β-strand	152-155	4	29
β-strand	161-163	3	29
β-strand	184-189	6	28
β-strand	194-199	6	28
β-strand	208-212	5	29
β-strand	228-232	5	29
β-strand	258-260	3	30
β-strand	266-267	2	31
β-strand	273-279	7	30
β-strand	284	1	32
β-strand	290	1	32
β-strand	292-297	6	29
β-strand	305-307	3	29
α-helix	312	1
β-strand	313	1	29
α-helix	314	1
β-strand	321-326	6	30
β-strand	329-334	6	30
β-strand	343-349	7	29
β-strand	356-357	2	29
β-strand	361-363	3	29
β-strand	364-365	2	31
β-strand	374-378	5	33
β-strand	381-383	3	34
β-strand	389-396	8	33
α-helix	400-402	3
β-strand	404-410	7	34
β-strand	416-422	7	34
β-strand	429-431	3	34
β-strand	439-444	6	33
β-strand	449-454	6	33
α-helix	459-461	3
β-strand	463-471	9	34
β-strand	476-480	5	34
β-strand	484-488	5	34

Chain C: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	35
β-strand	19-24	6	35
β-strand	30-35	6	36
β-strand	38-44	7	36
β-strand	50-54	5	35
α-helix	55-57	3
β-strand	60-66	7	36
α-helix	70-74	5
β-strand	75-80	6	36
α-helix	119-121	3
β-strand	122-126	5	37
β-strand	129-133	5	37
β-strand	142-146	5	36
β-strand	150-151	2	36
β-strand	160-163	4	37
β-strand	166-169	4	37
α-helix	174-177	4
β-strand	179-185	7	36
α-helix	190-192	3
β-strand	196-201	6	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Epidermal growth factor receptor	A	protein	627	Homo sapiens	P00533 (AlphaFold model)
LH-type bispecific diabody Ex3	B	protein	519	synthetic construct
T-cell surface glycoprotein CD3 gamma chain,T-cell surface glycoprotein CD3 epsilon chain	C	protein	204	Homo sapiens	P07766 (AlphaFold model), P09693 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9IPD_1 Epidermal growth factor receptor (chains A)
LEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQE
VAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEIL
HGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGE
ENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTC
PPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVR
KCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHT
PPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLN
ITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQ
VCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLP
QAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNC
TYGCTGPGLEGCPTNGPKIPSHHHHHH

Sequence of entity 2 (B), FASTA

>9IPD_2 LH-type bispecific diabody Ex3 (chains B)
MAFAADIQMTQSPSSLSASVGDRVTITCSASSSVSYMNWYQQTPGKAPKRWIYDTSKLAS
GVPSRFSGSGSGTDYTFTISSLQPEDIATYYCQQWSSNPFTFGQGTKLQITSGGGGQVQL
VQSGAEVKKPGASVKVSCKASGYTFTSYWMHWVRQAPGQGLEWMGNIWPGSGGTNYAEKF
KNRVTMTRDTSISTAYMELSRLRSDDTAVYYCARSGGPYFFDYWGQGTLVTVSSGGGGSG
GGGSGGGGSGGGGSDIVMTQSPLSLPVTPGEPASISCRSSQNIVHNNGITYLEWYLQKPG
QSPQLLIYKVSDRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHIPPTFGQG
TKVEIKSGGGGQVQLVQSGGGVVQPGRSLRLSCKASGYTFTRYTMHWVRQAPGKGLEWIG
YINPSRGYTNYNQKVKDRFTISRDNSKNTAFLQMDSLRPEDTGVYFCARYYDDHYSLDYW
GQGTPVTVSSAAAAEQKLISEEDLNLGGGMRGSHHHHHH

Sequence of entity 3 (C), FASTA

>9IPD_3 T-cell surface glycoprotein CD3 gamma chain,T-cell surface glycoprotein CD3 epsilon chain (chains C)
MQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDP
RGMYQCKGSQNKSKPLQVYYRMGSADDAKKDAAKKDDAKKDDAKKDGSDGNEEMGGITQT
PYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSG
YYVCYPRGSKPEDANFYLYLRARV

Primary citation

Bispecific antibody-antigen complex structures reveal activity enhancement by domain rearrangement. Sato, K., Uehara, S., Tsugita, A. et al. Cell Rep (2025) 44:115965-115965. DOI 10.1016/j.celrep.2025.115965 · PubMed

Other PDB entries of the same protein (UniProt P00533 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8A27 1.07 Å, EGFR kinase domain in complex with 2-(6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-1-yl)-2-[6-[2…
8A2D 1.11 Å, EGFR kinase domain (L858R/V948R) in complex with 2-[4-(difluoromethyl)-6-[2-[4-[[4-(hydro…
5UG9 1.33 Å, Crystal structure of the EGFR kinase domain (L858R, T790M, V948R) in complex with a…
5HG8 1.42 Å, EGFR (L858R, T790M, V948R) in complex with N-[3-({2-[(1-methyl-1H-pyrazol-4-yl)amino]-7H-…
8A2A 1.43 Å, EGFR kinase domain in complex with 2-(6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-1-yl)-2-[6-[2…
5UG8 1.46 Å, Crystal structure of the EGFR kinase domain (L858R, T790M, V948R) in complex with a…
3POZ 1.5 Å, EGFR Kinase domain complexed with tak-285
6TFV 1.5 Å, Crystal Structure of EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 18b
6TG0 1.5 Å, Crystal Structure of EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 21a
3VRP 1.52 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c in complex with…
5HG5 1.52 Å, EGFR (L858R, T790M, V948R) in complex with N-{3-[(2-{[4-(4-methylpiperazin-1-yl)phenyl]am…
5CNO 1.55 Å, Crystal structure of the EGFR kinase domain mutant V924R

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