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9y0t

Crystal structure of human MAIT A-F7 TCR-MR1*02-5-OP-RU complex

Method: X-RAY DIFFRACTION D_max: 169.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y0t
deposition_date	2025-08-29
title	Crystal structure of human MAIT A-F7 TCR-MR1*02-5-OP-RU complex
keywords	MAIT TCR, MR1, metabolite presentation, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

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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	49.64 Å
rg_electron	49.91 Å
i0	480375000.00
molecular_weight	180220.0 kDa
excluded_volume	224310 Å³
envelope_volume	319520 Å³
shell_volume	55073 Å³
envelope_diameter	176.7 Å
shell_rg	50.84 Å
envelope_rg	50.05 Å
shape_rg	49.91 Å
total_rg	49.93 Å
total_atoms	12724
n_residues	1612
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	169.0 Å
rg_real	50.03 Å
rg_real_error	2.53 Å
i0_real	4.8040e+08
i0_real_error	9.7180e+06
rg_reciprocal	49.65 Å
i0_reciprocal	480100000.0000
total_estimate	0.6015
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	42.2 Å
skewness	0.355
kurtosis	-0.639
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	36820000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 0.998; Sysdev: 0.000; Positv: 1.000; Valcen: 0.806; Smooth: 0.590

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Major histocompatibility complex class I-related protein 1
formula_weight	31730.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	13764

MRTHSLRYFRLGVSDPIRGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHWERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDFLIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRTEPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQAWASIELDPQSSNLYSCHVEHSGVHMVLQVP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Beta-2-microglobulin
formula_weight	11879.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	TCR alpha chain
formula_weight	22781.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,G

MGQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFSSFLSRSKGYSYLLLKELQMKDSASYLCAVKDSNYQLIWGAGTKLIIKPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	TCR beta chain
formula_weight	27677.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,H

MNAGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSVWTGEGSGELFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 non-polymer

description	1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol
formula_weight	330.3 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	843

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6. Citations (1)

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length_a	218.226 Å
length_b	71.054 Å
length_c	144.176 Å
angle_alpha	90.00 °
angle_beta	104.57 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.300 Å
resolution_low	46.620 Å
r_factor	0.1923
r_work	0.1910
r_free	0.2178

fit	/app/data/saxs_computation/y0/9y0t/9y0t.fit
pddf	/app/data/pr_computation/y0/9y0t/9y0t.pr.out
profile	/app/data/saxs_computation/y0/9y0t/9y0t.dat

Crystal structure of human MAIT A-F7 TCR-MR1*02-5-OP-RU complex

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

Diffraction

5. Entities & Polymer Info (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)