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9y0u

Crystal structure of human MAIT A-F7 TCR-MR1*03-5-OP-RU complex

Method: X-RAY DIFFRACTION D_max: 172.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y0u
deposition_date	2025-08-29
title	Crystal structure of human MAIT A-F7 TCR-MR1*03-5-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	49.74 Å
rg_electron	49.95 Å
i0	487282000.00
molecular_weight	181260.0 kDa
excluded_volume	225460 Å³
envelope_volume	319560 Å³
shell_volume	55042 Å³
envelope_diameter	179.0 Å
shell_rg	50.73 Å
envelope_rg	50.01 Å
shape_rg	49.94 Å
total_rg	50.01 Å
total_atoms	12782
n_residues	1613
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	172.9 Å
rg_real	50.11 Å
rg_real_error	1.90 Å
i0_real	4.8730e+08
i0_real_error	1.0240e+07
rg_reciprocal	49.74 Å
i0_reciprocal	487000000.0000
total_estimate	0.6253
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	37.8 Å
skewness	0.342
kurtosis	-0.651
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	36610000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 0.087; Positv: 1.000; Valcen: 0.771; Smooth: 0.762

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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	31697.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	14181

MRTHSLRYFRLGVSDPIHGVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHWERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDFLVFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRTEPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIVQEIDYGDILPSGDGTYQAWASIELDPQSSNLYSCHVEHSGVHMVLQVP

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	ACETIC ACID
formula_weight	60.1 kDa
src_method	syn
entity_count	2

Entity 6 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 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	8

Entity 8 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	3

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1080

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6. Citations (1)

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length_a	215.964 Å
length_b	69.919 Å
length_c	142.677 Å
angle_alpha	90.00 °
angle_beta	104.33 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.100 Å
resolution_low	47.790 Å
r_factor	0.1618
r_work	0.1614
r_free	0.1874

fit	/app/data/saxs_computation/y0/9y0u/9y0u.fit
pddf	/app/data/pr_computation/y0/9y0u/9y0u.pr.out
profile	/app/data/saxs_computation/y0/9y0u/9y0u.dat

Crystal structure of human MAIT A-F7 TCR-MR1*03-5-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)