SAXSdb — 9ru5

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1. Structure Basics

entry_id	9ru5
deposition_date	2025-07-03
title	Cryo-EM structure of TCRpub/pMHC
keywords	complex, IMMUNE SYSTEM; IMMUNE SYSTEM
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	29.66 Å
rg_electron	28.96 Å
i0	79409500.00
molecular_weight	68363.0 kDa
excluded_volume	84662 Å³
envelope_volume	107770 Å³
shell_volume	31843 Å³
envelope_diameter	96.6 Å
shell_rg	35.53 Å
envelope_rg	28.97 Å
shape_rg	28.95 Å
total_rg	29.62 Å
total_atoms	4825
n_residues	605
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	97.5 Å
rg_real	29.75 Å
rg_real_error	0.86 Å
i0_real	7.9410e+07
i0_real_error	1.3450e+06
rg_reciprocal	29.72 Å
i0_reciprocal	79410000.0000
total_estimate	0.8876
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	31.3 Å
skewness	0.394
kurtosis	-0.504
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	15520000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.968

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	TCRpub alpha chain
formula_weight	23175.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4825

QSVAQPEDQVNVAEGNPLTVKCTYSVSGNPYLFWYVQYPNRGLQFLLKYITGDNLVKGSYGFEAEFNKSQTSFHLKKPSALVSDSALYFCAVRVVTSGGSYIPTFGRGTSLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	TCRpub beta chain
formula_weight	27151.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPGRFSGRQFSNSRSEMNVSTLELGDSALYLCASSLAGDLGTEAFFGQGTRLTVVEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	MHC class I antigen
formula_weight	31909.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

HSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	ORF3a protein
formula_weight	1199.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

FTSDYYQLY

Source

organism	Severe acute respiratory syndrome coronavirus 2
common_name	2019-nCoV, SARS-CoV-2
ncbi_taxonomy_id	2697049
host_organism	Homo sapiens

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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	3.260 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.26 Å
resolution_method	—
num_particles	103583

fit	/app/data/saxs_computation/ru/9ru5/9ru5.fit
pddf	/app/data/pr_computation/ru/9ru5/9ru5.pr.out
profile	/app/data/saxs_computation/ru/9ru5/9ru5.dat

Cryo-EM structure of TCRpub/pMHC

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)