1N8Z: Extracellular domain of human HER2

Crystal structure of extracellular domain of human HER2 complexed with Herceptin Fab. Determined by X-ray diffraction at 2.52 Å resolution. Released 18 Feb 2003.

Method: X-ray diffraction
Resolution: 2.52 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 7,890
Mol. weight: 114.42 kDa
Ligands: NAG
Released: 18 Feb 2003

Explore 1N8Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1N8Z contains 37 α-helices and 113 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	144-148	5	5
β-strand	150	1	6
β-strand	153	1	6
β-strand	159-163	5	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-198	8	5
β-strand	205-210	6	5

Chain B: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-52	7	8
β-strand	57-60	4	8
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-98	7	8
β-strand	109-110	2	8
β-strand	114-118	5	8
β-strand	124	1	9
α-helix	125-126	2
β-strand	127-131	5	10
α-helix	135-137	3
β-strand	138-139	2	10
β-strand	142-152	11	10
β-strand	153	1	9
β-strand	158-161	4	11
α-helix	162-164	3
β-strand	170-172	3	10
α-helix	173-175	3
β-strand	176-177	2	10
α-helix	178	1
β-strand	183-192	10	10
α-helix	193-195	3
β-strand	196	1	12
β-strand	199	1	12
β-strand	202-207	6	11
α-helix	208-210	3
β-strand	212-217	6	11

Chain C: 21 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	13
β-strand	7	1	14
α-helix	12-14	3
α-helix	17-28	12
β-strand	33-35	3	13
β-strand	37	1	14
β-strand	38-41	4	15
α-helix	50-52	3
β-strand	57-58	2	13
β-strand	62-65	4	15
β-strand	79-80	2	13
β-strand	86	1	15
β-strand	90-95	6	15
β-strand	98	1	16
β-strand	114	1	16
β-strand	125-126	2	13
β-strand	130-134	5	15
α-helix	147-150	4
β-strand	151	1	13
α-helix	153-155	3
β-strand	160-162	3	15
α-helix	169-173	5
β-strand	182	1	17
β-strand	190	1	17
α-helix	191-193	3
β-strand	205	1	18
α-helix	210-212	3
β-strand	213	1	18
β-strand	218	1	19
β-strand	222	1	20
β-strand	230	1	20
β-strand	233	1	19
β-strand	236-238	3	21
β-strand	241-243	3	21
α-helix	246-248	3
β-strand	250-252	3	22
β-strand	259-261	3	22
β-strand	267-269	3	21
β-strand	272-274	3	21
β-strand	282-283	2	23
β-strand	288	1	21
β-strand	289-290	2	23
β-strand	297-301	5	23
β-strand	307-311	5	23
β-strand	321	1	24
β-strand	323	1	25
α-helix	326-328	3
α-helix	339-342	4
β-strand	347-348	2	26
β-strand	349	1	24
β-strand	351	1	25
β-strand	352-354	3	27
α-helix	356-358	3
α-helix	374-380	7
β-strand	383-384	2	26
β-strand	388-390	3	27
α-helix	401-403	3
β-strand	408-409	2	26
β-strand	415	1	27
β-strand	419-424	6	27
β-strand	438-439	2	26
β-strand	443-447	5	27
α-helix	460-463	4
β-strand	464	1	26
β-strand	471-474	4	27
α-helix	477-478	2
α-helix	479-484	6
β-strand	493	1	28
α-helix	494-496	3
β-strand	498	1	29
β-strand	506	1	29
β-strand	509	1	28
β-strand	512-514	3	30
β-strand	517-519	3	30
β-strand	531-534	4	30
β-strand	537-540	4	30
α-helix	541-542	2
β-strand	545	1	31
α-helix	546-548	3
β-strand	554	1	32
β-strand	562	1	32
β-strand	565	1	31
β-strand	568-570	3	33
β-strand	573-575	3	33
β-strand	593-595	3	34
β-strand	600	1	33
β-strand	601-603	3	34
α-helix	604	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Herceptin Fab (antibody) - light chain	A	protein	214	Mus musculus, Homo sapiens
Herceptin Fab (antibody) - heavy chain	B	protein	220	Mus musculus, Homo sapiens
Receptor protein-tyrosine kinase erbB-2	C	protein	607	Homo sapiens	P04626 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1N8Z_1 Herceptin Fab (antibody) - light chain (chains A)
DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B), FASTA

>1N8Z_2 Herceptin Fab (antibody) - heavy chain (chains B)
EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 3 (C), FASTA

>1N8Z_3 Receptor protein-tyrosine kinase erbB-2 (chains C)
TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQG
YVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQL
RSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGS
RCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSG
ICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEV
TAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFD
GDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYS
LTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPED
ECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLP
CHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGA
CQPCPIN

Ligands and cofactors

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

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure of the Extracellular Region of HER2 Alone and in Complex with the Herceptin Fab. Cho, H.-S., Mason, K., Ramyar, K.X. et al. Nature (2003) 421:756-760. DOI 10.1038/nature01392 · 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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1N8Z is part of these collections:

Antibodies and the immune system

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