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9qqe

Cryo-EM structure of the SN230G6 Fab - HLA-A*02:01 human alloantibody-HLA complex

Method: ELECTRON MICROSCOPY D_max: 133.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qqe
deposition_date	2025-03-31
title	Cryo-EM structure of the SN230G6 Fab - HLA-A*02:01 human alloantibody-HLA complex
keywords	Human Leucocyte Antigens, Alloantibody, Antibody, Antigen, Epitope, protein-protein interaction, organ rejection, 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	35.74 Å
rg_electron	36.14 Å
i0	119550000.00
molecular_weight	85607.0 kDa
excluded_volume	106110 Å³
envelope_volume	139740 Å³
shell_volume	35192 Å³
envelope_diameter	143.3 Å
shell_rg	38.15 Å
envelope_rg	36.83 Å
shape_rg	36.10 Å
total_rg	36.42 Å
total_atoms	6042
n_residues	769
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	133.8 Å
rg_real	36.29 Å
rg_real_error	1.84 Å
i0_real	1.1950e+08
i0_real_error	2.1080e+06
rg_reciprocal	35.95 Å
i0_reciprocal	119500000.0000
total_estimate	0.6883
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	33.4 Å
skewness	0.720
kurtosis	0.068
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	11190000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.488; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.482; Smooth: 0.000

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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	31854.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6042

GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Peptide VLHDDLLEA
formula_weight	1025.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

VLHDDLLEA

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Beta-2-microglobulin
formula_weight	11879.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	SN230G6 Fab Heavy Chain
formula_weight	25637.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EAQLVESGGGLVKPGGSLRLSCAASGFAFANHTMNWVRQAPGKGLEWVSSISISSTYIYYADSVKGRFSISRDNAKNSLYLQMNSLKAEDTAVYYCARDRPPLRIVGIWDYWGQGILVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHHHHHH

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 polymer

description	SN230G6 Fab Light Chain
formula_weight	22903.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

QSVLTQPPSASGTPGQRVTISCSGSSANIGSNIVDWYQHLPGTAPKLLIYSDNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCVAWDDSRYGYVFGTGTRVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
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	2.78 Å
resolution_method	—
num_particles	408487

fit	/app/data/saxs_computation/qq/9qqe/9qqe.fit
pddf	/app/data/pr_computation/qq/9qqe/9qqe.pr.out
profile	/app/data/saxs_computation/qq/9qqe/9qqe.dat

Cryo-EM structure of the SN230G6 Fab - HLA-A*02:01 human alloantibody-HLA 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

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)