HER2/ErbB2 extracellular domain (ECD) in extended conformation in complex with trastuzumab (TZB) antibody

Method: ELECTRON MICROSCOPY D_max: 83.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qbg
deposition_date	2025-03-02
last_revision	2025-08-06
title	HER2/ErbB2 extracellular domain (ECD) in extended conformation in complex with trastuzumab (TZB) antibody
keywords	Receptor, tyrosine kinase, transmembrane, HER2, SIGNALING PROTEIN; SIGNALING PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	26.53 Å
rg_electron	25.41 Å
i0	56883500.00
molecular_weight	56044.0 kDa
excluded_volume	68995 Å³
envelope_volume	83122 Å³
shell_volume	27734 Å³
envelope_diameter	87.1 Å
shell_rg	32.25 Å
envelope_rg	25.59 Å
shape_rg	25.37 Å
total_rg	26.23 Å
total_atoms	7684
n_residues	508
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	83.5 Å
rg_real	26.47 Å
rg_real_error	0.63 Å
i0_real	5.6880e+07
i0_real_error	7.7270e+05
rg_reciprocal	26.49 Å
i0_reciprocal	56880000.0000
total_estimate	0.9103
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.2 Å
skewness	0.242
kurtosis	-0.526
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	4101000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.994

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	Receptor tyrosine-protein kinase erbB-2,Green fluorescent protein
formula_weight	146753.2 kDa
ec_number	2.7.10.1
mutation	Del1-22,Del1030-1255,C789S,C805S,C965S.
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7684

MKFLVNVALVFMVVYISYIYADYKDDDDKHHHHHHHHHHLEVLFQGPYPYDVPDYSTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGISLTSTVQLVTQLMPYGSLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSESRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGLEVLFQGPGSMSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGMDELYK

Source

organism	Aequorea victoria
ncbi_taxonomy_id	6100
host_organism	Spodoptera frugiperda

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.60 Å
resolution_method	—
num_particles	77784

fit	/app/data/saxs_computation/qb/9qbg/9qbg.fit
pddf	/app/data/pr_computation/qb/9qbg/9qbg.pr.out
profile	/app/data/saxs_computation/qb/9qbg/9qbg.dat

HER2/ErbB2 extracellular domain (ECD) in extended conformation in complex with trastuzumab (TZB) antibody

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)