1S78: Receptor protein-tyrosine kinase erbB-2

Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex. Determined by X-ray diffraction at 3.25 Å resolution. Released 27 Apr 2004.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 15,481
Mol. weight: 235.73 kDa
Ligands: NAG
Released: 27 Apr 2004

Explore 1S78 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1S78 contains 73 α-helices and 210 β-strands across 6 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, 58 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	7	1	2
α-helix	12-14	3
α-helix	17-19	3
α-helix	20-28	9
β-strand	33-35	3	1
β-strand	37	1	2
β-strand	38-41	4	3
α-helix	50-52	3
β-strand	57-58	2	1
β-strand	62-65	4	3
β-strand	79-80	2	1
β-strand	86	1	3
β-strand	90-95	6	3
β-strand	117	1	4
β-strand	125-126	2	1
β-strand	130-134	5	3
β-strand	140	1	4
α-helix	147-150	4
β-strand	151	1	1
β-strand	160-163	4	3
α-helix	169-174	6
α-helix	187-189	3
α-helix	190-193	4
β-strand	205	1	5
α-helix	210-212	3
β-strand	213	1	5
α-helix	214-215	2
β-strand	218	1	6
β-strand	222	1	7
β-strand	230	1	7
β-strand	233	1	6
β-strand	236-238	3	8
β-strand	241-243	3	8
β-strand	250-251	2	9
β-strand	260-261	2	9
β-strand	267-269	3	8
β-strand	272-274	3	8
β-strand	282-284	3	10
β-strand	288	1	8
β-strand	289-290	2	10
α-helix	293-294	2
β-strand	297-301	5	10
β-strand	307-311	5	10
α-helix	312	1
α-helix	316-318	3
β-strand	320-321	2	11
β-strand	323	1	12
α-helix	326-328	3
α-helix	339-342	4
β-strand	347-349	3	11
β-strand	351	1	12
β-strand	352-354	3	13
α-helix	356-359	4
β-strand	362	1	14
β-strand	367	1	14
α-helix	372-379	8
β-strand	383-384	2	11
β-strand	388-390	3	13
β-strand	408-409	2	11
β-strand	415	1	13
β-strand	419-424	6	13
β-strand	438-439	2	11
β-strand	443-447	5	13
α-helix	460-462	3
β-strand	471-474	4	13
α-helix	479-483	5
β-strand	493	1	15
α-helix	494-496	3
β-strand	498	1	16
β-strand	506	1	16
β-strand	509	1	15
β-strand	512-514	3	17
β-strand	517-519	3	17
β-strand	531-533	3	18
β-strand	538-540	3	18
β-strand	554	1	19
α-helix	559-561	3
β-strand	562	1	19

Chain B: 25 helices, 62 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	20
β-strand	7	1	21
α-helix	12-14	3
α-helix	17-19	3
α-helix	20-28	9
β-strand	33-35	3	20
β-strand	37	1	21
β-strand	38-41	4	3
α-helix	50-52	3
β-strand	57-58	2	20
β-strand	62-65	4	3
β-strand	79-80	2	20
β-strand	86	1	3
β-strand	90-95	6	3
β-strand	117	1	22
β-strand	125-126	2	20
β-strand	130-134	5	3
β-strand	140	1	22
α-helix	147-150	4
β-strand	151	1	20
β-strand	160-163	4	3
α-helix	169-174	6
α-helix	187-189	3
α-helix	190-193	4
β-strand	205	1	23
α-helix	210-212	3
β-strand	213	1	23
α-helix	214-215	2
β-strand	218	1	24
β-strand	222	1	25
β-strand	230	1	25
β-strand	233	1	24
β-strand	236-238	3	26
β-strand	241-243	3	26
α-helix	246-248	3
β-strand	250-252	3	27
β-strand	259-261	3	27
β-strand	267-269	3	26
β-strand	272-274	3	26
β-strand	282-284	3	28
β-strand	288	1	26
β-strand	289-290	2	28
α-helix	293-294	2
β-strand	297-301	5	28
β-strand	307-311	5	28
α-helix	312	1
α-helix	316-318	3
β-strand	320-321	2	29
β-strand	323	1	30
α-helix	326-328	3
α-helix	339-342	4
β-strand	347-349	3	29
β-strand	351	1	30
β-strand	352-354	3	31
α-helix	356-359	4
β-strand	362	1	32
β-strand	367	1	32
α-helix	368-371	4
α-helix	372-380	9
β-strand	383-384	2	29
β-strand	388-390	3	31
β-strand	408-409	2	29
β-strand	415	1	31
β-strand	419-424	6	31
β-strand	438-439	2	29
β-strand	443-447	5	31
α-helix	460-462	3
β-strand	471-474	4	31
α-helix	479-484	6
β-strand	493	1	33
α-helix	494-496	3
β-strand	498	1	34
α-helix	503-505	3
β-strand	506	1	34
β-strand	509	1	33
β-strand	512-514	3	35
β-strand	517-519	3	35
β-strand	531-534	4	35
β-strand	537-540	4	35
α-helix	541-542	2
β-strand	545	1	36
α-helix	546-547	2
β-strand	554	1	37
β-strand	562	1	37
β-strand	565	1	36
β-strand	568	1	38
β-strand	575	1	38

Chain C: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	39
β-strand	10-13	4	40
β-strand	19-25	7	39
β-strand	33-38	6	40
α-helix	43-44	2
β-strand	45-49	5	40
β-strand	53-54	2	40
α-helix	55	1
β-strand	62-67	6	39
β-strand	70-75	6	39
α-helix	80-82	3
β-strand	85-90	6	40
α-helix	96	1
β-strand	97-98	2	40
β-strand	102-106	5	40
α-helix	119-121	3
β-strand	129-132	4	41
β-strand	136-139	4	42
β-strand	144-150	7	43
β-strand	153-154	2	43
β-strand	159-160	2	41
β-strand	163	1	42
α-helix	164-167	4
β-strand	173-175	3	42
β-strand	178-182	5	41
β-strand	192-198	7	43
β-strand	205	1	43

Chain D: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	44
β-strand	11-12	2	45
β-strand	18-25	8	44
α-helix	29-31	3
β-strand	34-39	6	40
β-strand	45-51	7	40
β-strand	57-59	3	40
α-helix	61-63	3
β-strand	67-72	6	44
α-helix	73-75	3
β-strand	77-82	6	44
α-helix	84-86	3
β-strand	88-95	8	40
β-strand	100-103	4	40
β-strand	107-109	3	40
β-strand	110-111	2	45
β-strand	120-124	5	46
β-strand	135-143	9	46
β-strand	145	1	47
β-strand	150-154	5	48
α-helix	155-157	3
β-strand	159	1	48
β-strand	163-165	3	46
α-helix	166-168	3
β-strand	169-170	2	47
β-strand	176-177	2	47
β-strand	180-185	6	46
β-strand	195-200	6	48
β-strand	205	1	48
β-strand	209-210	2	48

Chain E: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	49
β-strand	10-13	4	50
β-strand	19-25	7	49
β-strand	33-38	6	50
β-strand	45-49	5	50
β-strand	53-54	2	50
α-helix	55	1
β-strand	62-66	5	49
β-strand	70-75	6	49
α-helix	80-82	3
β-strand	85-90	6	50
α-helix	96	1
β-strand	97-98	2	50
β-strand	102-106	5	50
β-strand	111	1	51
β-strand	116-118	3	52
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	52
β-strand	140	1	51
β-strand	145-150	6	53
β-strand	153-154	2	53
β-strand	159-163	5	52
β-strand	173-182	10	52
α-helix	183-186	4
β-strand	191-197	7	53
β-strand	205-210	6	53
α-helix	211-213	3

Chain F: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	54
β-strand	11-12	2	55
β-strand	18-25	8	54
α-helix	29-31	3
β-strand	33-39	7	56
β-strand	46-51	6	56
β-strand	57-59	3	56
α-helix	61-63	3
β-strand	64	1	54
β-strand	67-72	6	54
β-strand	77-82	6	54
α-helix	84-86	3
β-strand	88-95	8	56
β-strand	100-103	4	56
β-strand	107-109	3	56
β-strand	110-111	2	55
α-helix	114-116	3
β-strand	117	1	57
α-helix	118-119	2
β-strand	120-124	5	58
β-strand	136-145	10	58
β-strand	146	1	57
β-strand	151-154	4	59
α-helix	155-157	3
β-strand	159	1	59
β-strand	163-165	3	58
α-helix	166-168	3
β-strand	169-170	2	58
β-strand	176-184	9	58
α-helix	186-188	3
β-strand	194-200	7	59
β-strand	205-211	7	59

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor protein-tyrosine kinase erbB-2	A, B	protein	624	Homo sapiens	P04626 (AlphaFold model)
Pertuzumab Fab light chain	C, E	protein	214	Mus musculus	Q7Z3Y4 (AlphaFold model)
Pertuzumab Fab heavy chain	D, F	protein	226	Mus musculus

Sequence of entity 1 (A, B), FASTA

>1S78_1 Receptor protein-tyrosine kinase erbB-2 (chains A, B)
TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQG
YVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQL
RSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGS
RCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSG
ICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEV
TAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFD
GDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYS
LTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPED
ECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLP
CHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGA
CQPCPINCTHSCVDLDDKGCPAEQ

Sequence of entity 2 (C, E), FASTA

>1S78_2 Pertuzumab Fab light chain (chains C, E)
DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQQKPGKAPKLLIYSASYRYTGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (D, F), FASTA

>1S78_3 Pertuzumab Fab heavy chain (chains D, F)
EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRQAPGKGLEWVADVNPNSGGSIY
NQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Ligands and cofactors

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

Primary citation

Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex. Franklin, M.C., Carey, K.D., Vajdos, F.F. et al. Cancer Cell (2004) 5:317-328. DOI 10.1016/S1535-6108(04)00083-2 · 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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1S78 is part of these collections:

Antibodies and the immune system

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