7SYD: Extracellular module of the full-length EGFR

Cryo-EM structure of the extracellular module of the full-length EGFR bound to EGF "tips-juxtaposed" conformation. Determined by electron microscopy at 3.1 Å resolution. Released 22 Dec 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,216
Mol. weight: 281.32 kDa
Released: 22 Dec 2021

Explore 7SYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SYD contains 42 α-helices and 149 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: 18 helices, 66 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	6-7	2	1
β-strand	10	1	2
β-strand	16	1	3
α-helix	20-30	11
β-strand	36-37	2	1
β-strand	40	1	2
β-strand	41-44	4	4
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	101	1	6
β-strand	107	1	6
β-strand	110	1	5
β-strand	118-119	2	1
β-strand	123-127	5	4
β-strand	144	1	1
α-helix	146-148	3
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
β-strand	207	1	8
α-helix	208-209	2
β-strand	212	1	9
β-strand	216	1	10
α-helix	221-223	3
β-strand	224	1	10
β-strand	227	1	9
α-helix	240-242	3
β-strand	244-247	4	11
β-strand	252-255	4	11
β-strand	261-263	3	12
β-strand	266-268	3	12
β-strand	276-277	2	13
β-strand	282	1	12
β-strand	283-284	2	13
β-strand	291-296	6	13
β-strand	299-304	6	13
α-helix	305	1
α-helix	309-311	3
β-strand	313-314	2	14
β-strand	316	1	15
α-helix	319-321	3
α-helix	332-335	4
β-strand	341-342	2	14
β-strand	344	1	15
β-strand	345-347	3	16
β-strand	355	1	17
β-strand	360	1	17
α-helix	361-364	4
α-helix	365-373	9
β-strand	376-377	2	14
β-strand	381-383	3	16
β-strand	401-402	2	14
β-strand	408	1	16
β-strand	412-417	6	16
β-strand	431-432	2	14
β-strand	436-440	5	16
β-strand	457	1	14
β-strand	464	1	16
α-helix	472-476	5
β-strand	486	1	18
β-strand	491	1	19
α-helix	496-498	3
β-strand	499	1	19
β-strand	502	1	18
β-strand	505-507	3	20
β-strand	510-512	3	20
α-helix	523	1
β-strand	524-527	4	21
β-strand	530-533	4	21
α-helix	534-535	2
α-helix	552-554	3
β-strand	561	1	22
β-strand	568	1	22
β-strand	575-576	2	23
β-strand	582-583	2	23
β-strand	586	1	24
β-strand	594	1	24

Chain B: 20 helices, 75 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	6-7	2	26
β-strand	10	1	27
β-strand	16-17	2	28
α-helix	20-31	12
β-strand	36-37	2	26
β-strand	40	1	27
β-strand	41-44	4	29
α-helix	46-47	2
α-helix	53-56	4
β-strand	60-61	2	26
β-strand	65-68	4	29
β-strand	74	1	30
β-strand	82-83	2	26
β-strand	89	1	29
β-strand	93-98	6	29
β-strand	110	1	30
β-strand	118-119	2	26
β-strand	123-127	5	29
β-strand	144	1	26
β-strand	153-154	2	29
α-helix	165-167	3
α-helix	171-173	3
β-strand	175	1	31
β-strand	183	1	31
β-strand	199	1	32
β-strand	207	1	32
α-helix	208-209	2
β-strand	212	1	33
β-strand	216	1	34
β-strand	224	1	34
β-strand	227	1	33
β-strand	230-231	2	35
β-strand	236-237	2	35
α-helix	240-242	3
β-strand	244-247	4	36
β-strand	252-255	4	36
β-strand	261-263	3	37
β-strand	266-268	3	37
β-strand	276-277	2	38
β-strand	282	1	37
β-strand	283-284	2	38
β-strand	291-294	4	38
α-helix	295	1
β-strand	300-304	5	38
β-strand	313	1	39
β-strand	316	1	40
β-strand	318	1	41
β-strand	321	1	41
α-helix	332-335	4
β-strand	341	1	39
β-strand	344	1	40
β-strand	345-347	3	42
α-helix	349-353	5
β-strand	355	1	43
β-strand	360	1	43
α-helix	361-364	4
α-helix	365-373	9
β-strand	376-377	2	39
β-strand	381-383	3	42
α-helix	394-396	3
β-strand	401-402	2	39
β-strand	408	1	42
β-strand	412-417	6	42
β-strand	423	1	44
β-strand	431-432	2	39
β-strand	436-440	5	42
β-strand	447	1	44
α-helix	453-456	4
β-strand	457	1	39
β-strand	464-465	2	42
α-helix	474-477	4
β-strand	486	1	45
β-strand	491	1	46
β-strand	499	1	46
β-strand	502	1	45
β-strand	505-506	2	47
β-strand	511-512	2	47
β-strand	524-527	4	48
β-strand	530-533	4	48
α-helix	534-535	2
β-strand	538	1	49
β-strand	547	1	50
α-helix	552-554	3
β-strand	555	1	50
β-strand	558	1	49
β-strand	561-563	3	51
β-strand	566-568	3	51
β-strand	573	1	52
α-helix	578-580	3
β-strand	584	1	52
β-strand	585-587	3	53
β-strand	592	1	51
β-strand	593-595	3	53
α-helix	608-611	4

Chain C: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	19-23	5	3
β-strand	28-32	5	3
α-helix	33-34	2
β-strand	37-38	2	25
β-strand	44-45	2	25

Chain D: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	19-23	5	28
β-strand	28-33	6	28
α-helix	34	1
β-strand	37-38	2	54
β-strand	44-45	2	54

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Epidermal growth factor receptor	A, B	protein	1210	Homo sapiens	P00533 (AlphaFold model)
Epidermal growth factor	C, D	protein	53	Homo sapiens	P01133 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7SYD_1 Epidermal growth factor receptor (chains A, B)
MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEV
VLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALA
VLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDF
QNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGC
TGPRESDCLVCRKFRNEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYV
VTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFK
NCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAF
ENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKL
FGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCN
LLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVM
GENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVV
ALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPNQALLRILKETEFKKIKVLGS
GAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGI
CLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAA
RNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSY
GVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPK
FRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQ
QGFFSSPSTSRTPLLSSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTED
SIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLN
TVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGSTAENAEYLRV
APQSSEFIGA

Sequence of entity 2 (C, D), FASTA

>7SYD_2 Epidermal growth factor (chains C, D)
NSDSECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWELR

Primary citation

A molecular mechanism for the generation of ligand-dependent differential outputs by the epidermal growth factor receptor. Huang, Y., Ognjenovic, J., Karandur, D. et al. Elife (2021) 10. DOI 10.7554/eLife.73218 · 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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