3NJP: Epidermal growth factor receptor

The Extracellular and Transmembrane Domain Interfaces in Epidermal Growth Factor Receptor Signaling. Determined by X-ray diffraction at 3.3 Å resolution. Released 13 Oct 2010.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,567
Mol. weight: 151.81 kDa
Ligands: NAG, 2PE
Released: 13 Oct 2010

Explore 3NJP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NJP contains 50 α-helices and 153 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: 23 helices, 73 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	1
β-strand	10	1	2
β-strand	16-17	2	3
α-helix	20-31	12
β-strand	36-37	2	1
β-strand	40	1	2
β-strand	41-44	4	4
α-helix	53-57	5
β-strand	60-61	2	1
β-strand	65-68	4	4
β-strand	74	1	5
β-strand	82-83	2	1
β-strand	89	1	4
β-strand	93-98	6	4
β-strand	110	1	5
β-strand	118	1	1
β-strand	119	1	6
β-strand	123-127	5	4
α-helix	135-137	3
α-helix	140-143	4
β-strand	144	1	6
β-strand	153-154	2	4
α-helix	171-173	3
β-strand	175	1	7
β-strand	183	1	7
β-strand	199	1	8
α-helix	204-206	3
β-strand	207	1	8
α-helix	208-209	2
β-strand	212	1	9
β-strand	216	1	10
β-strand	224	1	10
β-strand	227	1	9
β-strand	230-232	3	11
β-strand	235-237	3	11
α-helix	240-242	3
β-strand	244-247	4	12
β-strand	252-255	4	12
β-strand	261-263	3	11
β-strand	266-268	3	11
β-strand	276-277	2	13
β-strand	282	1	11
β-strand	283-284	2	13
β-strand	293-296	4	13
β-strand	299-302	4	13
α-helix	309-312	4
β-strand	313-314	2	14
α-helix	315	1
β-strand	316	1	15
α-helix	319-321	3
α-helix	331-335	5
β-strand	340-342	3	14
β-strand	344	1	15
β-strand	345-347	3	16
α-helix	349-353	5
β-strand	355	1	17
β-strand	360	1	17
α-helix	361-363	3
α-helix	365-373	9
β-strand	376-377	2	14
β-strand	381-383	3	16
β-strand	392	1	18
α-helix	394-396	3
β-strand	401-402	2	14
β-strand	408	1	16
β-strand	412-417	6	16
β-strand	423	1	18
β-strand	431-432	2	14
β-strand	436-440	5	16
α-helix	448-450	3
α-helix	453-456	4
β-strand	464-465	2	16
α-helix	472-477	6
β-strand	486	1	19
β-strand	491	1	20
β-strand	499	1	20
β-strand	502	1	19
β-strand	505-507	3	21
β-strand	510-512	3	21
β-strand	524-527	4	21
β-strand	530-533	4	21
α-helix	534-535	2
β-strand	538	1	22
β-strand	547	1	23
α-helix	552-554	3
β-strand	555	1	23
β-strand	558	1	22
β-strand	561-563	3	24
β-strand	566-568	3	24
β-strand	573-576	4	25
α-helix	578-580	3
β-strand	582-584	3	25
β-strand	585-587	3	26
β-strand	592	1	24
β-strand	593-595	3	26
α-helix	609-611	3

Chain B: 25 helices, 72 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	6-7	2	27
β-strand	10	1	28
β-strand	16-17	2	29
α-helix	20-31	12
β-strand	36-37	2	27
β-strand	40	1	28
β-strand	41-44	4	30
α-helix	46-47	2
α-helix	53-56	4
β-strand	60-61	2	27
β-strand	65-68	4	30
β-strand	74	1	31
β-strand	82-83	2	27
β-strand	89	1	30
β-strand	93-98	6	30
β-strand	110	1	31
β-strand	118-119	2	27
β-strand	123-127	5	30
α-helix	135-137	3
α-helix	140-143	4
β-strand	144	1	27
α-helix	149-151	3
β-strand	153-154	2	30
α-helix	171-173	3
β-strand	175	1	32
β-strand	183	1	32
β-strand	199	1	33
α-helix	204-206	3
β-strand	207	1	33
α-helix	208-209	2
β-strand	212	1	34
β-strand	216	1	35
β-strand	224	1	35
β-strand	227	1	34
β-strand	231	1	36
β-strand	232	1	37
β-strand	235	1	37
β-strand	244-247	4	38
β-strand	252-255	4	38
β-strand	261-263	3	36
β-strand	266-268	3	36
β-strand	276-277	2	39
β-strand	282	1	36
β-strand	283-284	2	39
β-strand	291-294	4	39
β-strand	300-304	5	39
α-helix	309-312	4
β-strand	313-314	2	40
α-helix	315	1
α-helix	319-321	3
α-helix	331-335	5
β-strand	340-342	3	40
β-strand	345-347	3	41
α-helix	349-352	4
β-strand	355	1	42
β-strand	360	1	42
α-helix	361-363	3
α-helix	365-373	9
β-strand	376-377	2	40
β-strand	381-383	3	41
β-strand	392	1	43
α-helix	394-396	3
β-strand	401-402	2	40
β-strand	408	1	41
β-strand	412-417	6	41
β-strand	423	1	43
β-strand	431-432	2	40
β-strand	436-440	5	41
α-helix	448-450	3
α-helix	453-456	4
β-strand	457	1	40
β-strand	464-465	2	41
α-helix	476-478	3
β-strand	486	1	44
β-strand	491	1	45
α-helix	496-498	3
β-strand	499	1	45
β-strand	502	1	44
β-strand	505-506	2	46
β-strand	511-512	2	46
β-strand	524-527	4	47
β-strand	530-533	4	47
α-helix	534-535	2
β-strand	538	1	48
β-strand	547	1	49
α-helix	552-554	3
β-strand	555	1	49
β-strand	558	1	48
β-strand	561-563	3	50
β-strand	566-568	3	50
β-strand	573	1	51
α-helix	578-580	3
β-strand	584	1	51
β-strand	585-587	3	52
β-strand	592	1	50
β-strand	593-595	3	52

Chains C and D: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	19-23	5	3
β-strand	28-33	6	3
α-helix	34	1
β-strand	37-38	2	53
β-strand	44-45	2	53

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Epidermal growth factor receptor	A, B	protein	614	Homo sapiens	P00533 (AlphaFold model)
Epidermal growth factor	C, D	protein	47	Homo sapiens	P01133 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3NJP_1 Epidermal growth factor receptor (chains A, B)
LEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQE
VAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEIL
HGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGE
ENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTC
PPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVR
KCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHT
PPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLN
ITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQ
VCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCKLLEGEPREFVENSECIQCHPECLP
QAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNC
TYGCTGPGLEGCPT

Sequence of entity 2 (C, D), FASTA

>3NJP_2 Epidermal growth factor (chains C, D)
ECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12
2PE	Nonaethylene glycol	C18 H38 O10	5

Primary citation

Structural evidence for loose linkage between ligand binding and kinase activation in the epidermal growth factor receptor. Lu, C., Mi, L.Z., Grey, M.J. et al. Mol Cell Biol (2010) 30:5432-5443. DOI 10.1128/MCB.00742-10 · 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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