3H3B: Receptor tyrosine-protein kinase erbB-2

Crystal structure of the single-chain Fv (scFv) fragment of an anti-ErbB2 antibody chA21 in complex with residues 1-192 of ErbB2 extracellular domain. Determined by X-ray diffraction at 2.45 Å resolution. Released 28 Apr 2010.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 6,907
Mol. weight: 98.46 kDa
Released: 28 Apr 2010

Explore 3H3B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3H3B contains 28 α-helices and 84 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: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
α-helix	12-14	3
α-helix	17-28	12
β-strand	33-35	3	1
β-strand	38-41	4	2
α-helix	50-52	3
β-strand	57-58	2	1
β-strand	62-65	4	2
β-strand	71-73	3	3
β-strand	79-80	2	1
β-strand	86	1	2
β-strand	90-95	6	2
β-strand	98	1	4
α-helix	105-107	3
β-strand	114	1	4
β-strand	117-119	3	3
β-strand	125-126	2	1
β-strand	130-134	5	2
α-helix	147-150	4
β-strand	151	1	1
β-strand	160-162	3	2
α-helix	169-174	6
β-strand	182	1	5
β-strand	190	1	5

Chain B: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	6
α-helix	12-14	3
α-helix	17-28	12
β-strand	33-35	3	6
β-strand	38-41	4	7
α-helix	50-52	3
β-strand	57-58	2	6
β-strand	62-65	4	7
β-strand	71-73	3	8
β-strand	79-80	2	6
β-strand	86	1	7
β-strand	90-95	6	7
β-strand	98	1	9
β-strand	114	1	9
β-strand	117-119	3	8
β-strand	125-126	2	6
β-strand	130-134	5	7
α-helix	142-144	3
α-helix	147-150	4
β-strand	151	1	6
β-strand	160-162	3	7
α-helix	169-174	6
β-strand	182	1	10
α-helix	187-189	3
β-strand	190	1	10

Chain C: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	0-2	3
β-strand	4-7	4	11
β-strand	10-12	3	12
β-strand	19-25	7	11
β-strand	30-31	2	13
β-strand	36-37	2	13
β-strand	39-44	6	12
β-strand	51-55	5	12
β-strand	59-60	2	12
α-helix	61	1
β-strand	68-73	6	11
β-strand	76-81	6	11
α-helix	86-88	3
β-strand	91-96	6	12
α-helix	102	1
β-strand	103-104	2	12
β-strand	108-111	4	12
β-strand	137-140	4	14
α-helix	141-143	3
β-strand	144-146	3	15
β-strand	152-159	8	14
α-helix	163-165	3
β-strand	167-173	7	15
β-strand	180-186	7	15
β-strand	192-194	3	15
α-helix	196-198	3
β-strand	202-207	6	14
β-strand	212-217	6	14
α-helix	222-224	3
β-strand	226-233	8	15
α-helix	236-238	3
β-strand	241-244	4	15
β-strand	248-252	5	15

Chain D: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	-1-3	5
β-strand	4-7	4	16
β-strand	10-13	4	17
β-strand	19-25	7	16
β-strand	30-31	2	18
β-strand	36-37	2	18
β-strand	39-44	6	17
β-strand	51-55	5	17
β-strand	59-60	2	17
α-helix	61	1
β-strand	68-73	6	16
β-strand	76-81	6	16
β-strand	91-96	6	17
α-helix	102	1
β-strand	103-104	2	17
β-strand	108-112	5	17
β-strand	137-140	4	19
β-strand	144-146	3	20
β-strand	152-159	8	19
α-helix	163-165	3
β-strand	167-173	7	20
β-strand	180-186	7	20
β-strand	192-194	3	20
β-strand	202-207	6	19
β-strand	212-217	6	19
α-helix	222-224	3
β-strand	226-233	8	20
α-helix	236-238	3
β-strand	241-244	4	20
β-strand	248-252	5	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor tyrosine-protein kinase erbB-2	A, B	protein	194	Homo sapiens	P04626 (AlphaFold model)
anti-ErbB2 antibody chA21	C, D	protein	259	Mus musculus

Sequence of entity 1 (A, B), FASTA

>3H3B_1 Receptor tyrosine-protein kinase erbB-2 (chains A, B)
GSTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEV
QGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLREL
QLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCK
GSRCWGESSEDCQS

Sequence of entity 2 (C, D), FASTA

>3H3B_2 anti-ErbB2 antibody chA21 (chains C, D)
AAQPADIVLTQTPSSLPVSVGEKVTMTCKSSQTLLYSNNQKNYLAWYQQKPGQSPKLLIS
WAFTRKSGVPDRFTGSGSGTDFTLTIGSVKAEDLAVYYCQQYSNYPWTFGGGTRLEIKRG
GGGSGGGGSGGGGSGGGGSEVQLQQSGPEVVKTGASVKISCKASGYSFTGYFINWVKKNS
GKSPEWIGHISSSYATSTYNQKFKNKAAFTVDTSSSTAFMQLNSLTSEDSAVYYCVRSGN
YEEYAMDYWGQGTSVTVSS

Primary citation

Structural Insights into the Down-regulation of Overexpressed p185her2/neu Protein of Transformed Cells by the Antibody chA21. Zhou, H., Zha, Z., Liu, Y. et al. J Biol Chem (2011) 286:31676-31683. DOI 10.1074/jbc.M111.235184 · 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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