SAXSdb — 9rup

▼

1. Structure Basics

entry_id	9rup
deposition_date	2025-07-04
title	Cryo-EM structure of TCRpub/pMHC dimer
keywords	complex, IMMUNE SYSTEM; IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	42.06 Å
rg_electron	41.83 Å
i0	524803000.00
molecular_weight	181370.0 kDa
excluded_volume	224200 Å³
envelope_volume	325450 Å³
shell_volume	65803 Å³
envelope_diameter	151.0 Å
shell_rg	46.33 Å
envelope_rg	41.03 Å
shape_rg	41.82 Å
total_rg	42.09 Å
total_atoms	12807
n_residues	1596
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

▼

3. P(r) Analysis (GNOM)

dmax	144.2 Å
rg_real	42.16 Å
rg_real_error	1.36 Å
i0_real	5.2480e+08
i0_real_error	9.8350e+06
rg_reciprocal	42.06 Å
i0_reciprocal	524700000.0000
total_estimate	0.8495
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.3 Å
skewness	0.497
kurtosis	-0.052
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	54540000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.762

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	T cell receptor, alpha chain
formula_weight	23175.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,a
atom_count	12807

QSVAQPEDQVNVAEGNPLTVKCTYSVSGNPYLFWYVQYPNRGLQFLLKYITGDNLVKGSYGFEAEFNKSQTSFHLKKPSALVSDSALYFCAVRVVTSGGSYIPTFGRGTSLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	T cell receptor, beta chain
formula_weight	27151.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,b

GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPGRFSGRQFSNSRSEMNVSTLELGDSALYLCASSLAGDLGTEAFFGQGTRLTVVEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Beta-2-microglobulin
formula_weight	11748.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,e

IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	MHC class I antigen
formula_weight	31909.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,c

HSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 polymer

description	ORF3a_207-215 epitope
formula_weight	1199.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,d

FTSDYYQLY

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

▶

6. Citations (1)

▶

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	4.110 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.11 Å
resolution_method	—
num_particles	91648

fit	/app/data/saxs_computation/ru/9rup/9rup.fit
pddf	/app/data/pr_computation/ru/9rup/9rup.pr.out
profile	/app/data/saxs_computation/ru/9rup/9rup.dat

Cryo-EM structure of TCRpub/pMHC dimer

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)