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9qcd

Micro-ED structure of the NSH2-CSH2 tandem domain of SHP2 in complex with the bis-phosphorylated pY627-pY659-Gab1 (613-694) peptide

Method: ELECTRON CRYSTALLOGRAPHY D_max: 74.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qcd
deposition_date	2025-03-04
title	Micro-ED structure of the NSH2-CSH2 tandem domain of SHP2 in complex with the bis-phosphorylated pY627-pY659-Gab1 (613-694) peptide
keywords	SH2-domain, phosphatase, PTPN11, phospho-tyrosine, SIGNALING PROTEIN; SIGNALING PROTEIN
method	ELECTRON CRYSTALLOGRAPHY

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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	21.09 Å
rg_electron	20.26 Å
i0	13893900.00
molecular_weight	27436.0 kDa
excluded_volume	34138 Å³
envelope_volume	42543 Å³
shell_volume	18200 Å³
envelope_diameter	75.7 Å
shell_rg	25.71 Å
envelope_rg	20.42 Å
shape_rg	20.23 Å
total_rg	21.14 Å
total_atoms	3821
n_residues	239
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	74.1 Å
rg_real	21.13 Å
rg_real_error	0.55 Å
i0_real	1.3890e+07
i0_real_error	2.1230e+05
rg_reciprocal	21.13 Å
i0_reciprocal	13890000.0000
total_estimate	0.8527
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.9 Å
skewness	0.423
kurtosis	-0.231
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	3151000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.729; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Tyrosine-protein phosphatase non-receptor type 11
formula_weight	25133.2 kDa
ec_number	3.1.3.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	3821

SMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRIN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	GRB2-associated-binding protein 1
formula_weight	7707.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GPIKPKGDKQVEYLDLDLDSGKSTPPRKQKSSGSGSSVADERVDYVVVDQQKTLALKSTREAWTDGRQS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

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6. Citations (2)

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length_a	30.595 Å
length_b	82.253 Å
length_c	117.764 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	3.200 Å
resolution_low	33.720 Å
r_factor	0.3032
r_work	0.3005
r_free	0.3527

resolution	3.20 Å
resolution_method	—
num_particles	—

fit	/app/data/saxs_computation/qc/9qcd/9qcd.fit
pddf	/app/data/pr_computation/qc/9qcd/9qcd.pr.out
profile	/app/data/saxs_computation/qc/9qcd/9qcd.dat

Micro-ED structure of the NSH2-CSH2 tandem domain of SHP2 in complex with the bis-phosphorylated pY627-pY659-Gab1 (613-694) peptide

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

Refinement

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)