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

Method: ELECTRON MICROSCOPY D_max: 81.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qbf
deposition_date	2025-03-02
last_revision	2025-08-06
title	HER2/ErbB2 extracellular domain (ECD) in compact 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	25.19 Å
rg_electron	24.01 Å
i0	56137400.00
molecular_weight	55691.0 kDa
excluded_volume	68554 Å³
envelope_volume	80508 Å³
shell_volume	27936 Å³
envelope_diameter	83.9 Å
shell_rg	31.24 Å
envelope_rg	24.60 Å
shape_rg	23.99 Å
total_rg	24.85 Å
total_atoms	7628
n_residues	504
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	81.3 Å
rg_real	25.13 Å
rg_real_error	0.67 Å
i0_real	5.6140e+07
i0_real_error	8.4090e+05
rg_reciprocal	25.15 Å
i0_reciprocal	56140000.0000
total_estimate	0.9000
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.7 Å
skewness	0.269
kurtosis	-0.381
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	3842000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.991

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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	146737.2 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	7628

MKFLVNVALVFMVVYISYIYADYKDDDDKHHHHHHHHHHLEVLFQGPYPYDVPDYATQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGISLTSTVQLVTQLMPYGSLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSESRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGLEVLFQGPGSMSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGMDELYK

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	3.80 Å
resolution_method	—
num_particles	91370

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

HER2/ErbB2 extracellular domain (ECD) in compact 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)