SAXSdb — 9rxm

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1. Structure Basics

entry_id	9rxm
deposition_date	2025-07-11
title	Cryo-EM structure of TCRpriv/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	34.46 Å
rg_electron	34.83 Å
i0	119817000.00
molecular_weight	85881.0 kDa
excluded_volume	106450 Å³
envelope_volume	134020 Å³
shell_volume	34825 Å³
envelope_diameter	134.2 Å
shell_rg	37.47 Å
envelope_rg	35.77 Å
shape_rg	34.82 Å
total_rg	35.03 Å
total_atoms	6063
n_residues	752
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	124.5 Å
rg_real	34.93 Å
rg_real_error	1.34 Å
i0_real	1.1980e+08
i0_real_error	2.1480e+06
rg_reciprocal	34.64 Å
i0_reciprocal	119800000.0000
total_estimate	0.7788
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.5 Å
skewness	0.706
kurtosis	0.004
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	13960000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.569; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.667; Smooth: 0.745

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	T cell receptor alpha chain
formula_weight	22990.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6063

QQVMQIPQYQHVQEGEDFTTYCNSSTTLSNIQWYKQRPGGHPVFLIQLVKSGEVKKQKRLTFQFGEAKKNSSLHITATQTTDVGTYFCASDREGGSEKLVFGKGTKLTVNPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	T cell receptor beta chain
formula_weight	27238.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPGRFSGRQFSNSRSEMNVSTLELGDSALYLCASSLWTGVGTEAFFGQGTRLTVVEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	SARS-CoV-2 ORF3a_207-215 epitope
formula_weight	1199.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

FTSDYYQLY

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	MHC class I antigen
formula_weight	31492.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

HSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 polymer

description	Beta-2-microglobulin
formula_weight	11748.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
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	3.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.00 Å
resolution_method	—
num_particles	457735

fit	/app/data/saxs_computation/rx/9rxm/9rxm.fit
pddf	/app/data/pr_computation/rx/9rxm/9rxm.pr.out
profile	/app/data/saxs_computation/rx/9rxm/9rxm.dat

Cryo-EM structure of TCRpriv/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 (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)