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9qg8

Crystal structure of the great reed warbler MHC class I in complex with an 8-mer peptide

Method: X-RAY DIFFRACTION D_max: 77.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qg8
deposition_date	2025-03-13
title	Crystal structure of the great reed warbler MHC class I in complex with an 8-mer peptide
keywords	MHC class I, great reed warbler, antigen 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	24.30 Å
rg_electron	23.19 Å
i0	34562900.00
molecular_weight	44381.0 kDa
excluded_volume	54999 Å³
envelope_volume	67561 Å³
shell_volume	24347 Å³
envelope_diameter	80.0 Å
shell_rg	30.15 Å
envelope_rg	23.24 Å
shape_rg	23.19 Å
total_rg	24.02 Å
total_atoms	3131
n_residues	380
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	77.2 Å
rg_real	24.26 Å
rg_real_error	0.47 Å
i0_real	3.4560e+07
i0_real_error	4.3930e+05
rg_reciprocal	24.27 Å
i0_reciprocal	34560000.0000
total_estimate	0.9080
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.2 Å
skewness	0.262
kurtosis	-0.493
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	7364000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	MHC class I antigen
formula_weight	31630.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3221

MVLHSLHYLDVAVSEPSPGIPQFVAMGFVDGIPFTRYDSERGRMEPLTEWIKDSADPEYWDSQTQIGVGSQHVYARSLETLRERYNQSGGLHTVLRVYGCELLSDGSVRGSERFGYDGRDFISFDLESGRFMAADSAAEITRRRWEHEGIVAERQTNYLKHECPEWLQKYVGYGQKELERKEPPDVHVSGKEEHGTLILSCHAYGFYPKTIAVNWMKGDEIWDQETEWGGVVPNSDGTFHTWARIEALPEEREQYRCRVEHPGMPEPGIFAWEPT

Source

organism	Acrocephalus arundinaceus
common_name	great reed warbler
ncbi_taxonomy_id	39621
host_organism	Escherichia coli

Entity 2 polymer

description	Beta-2-microglobulin
formula_weight	14206.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MHHHHHHSSGVDLGTENLYFQSMAGEAPKVEVYARSRAEEGKENILHCFITGFHPPKIDVELLKNGEPMPGVTYGDLSFNDKWQFQRLVYVPFIPTREDIFTCRVAHSTMPEPRSYRWEPDF

Source

organism	Acrocephalus arundinaceus
common_name	great reed warbler
ncbi_taxonomy_id	39621
host_organism	Escherichia coli

Entity 3 polymer

description	LYS-THR-MET-MET-ALA-HIS-ASP-LEU
formula_weight	948.2 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

KTMMAHDL

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	6

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	85

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6. Citations (1)

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length_a	205.947 Å
length_b	49.038 Å
length_c	39.380 Å
angle_alpha	90.00 °
angle_beta	94.69 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.150 Å
resolution_low	47.700 Å
r_factor	0.2089
r_work	0.2057
r_free	0.2658

fit	/app/data/saxs_computation/qg/9qg8/9qg8.fit
pddf	/app/data/pr_computation/qg/9qg8/9qg8.pr.out
profile	/app/data/saxs_computation/qg/9qg8/9qg8.dat

Crystal structure of the great reed warbler MHC class I in complex with an 8-mer peptide

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)