SAXSdb — 9qqf

▼

1. Structure Basics

entry_id	9qqf
deposition_date	2025-03-31
title	Cryo-EM structure of the WIM8E5 Fab - HLA-A*11:01 human alloantibody-HLA complex
keywords	Human Leucocyte Antigens, Alloantibody, Antibody, Antigen, Epitope, protein-protein interaction, organ rejection, IMMUNE SYSTEM; IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	35.88 Å
rg_electron	36.25 Å
i0	126471000.00
molecular_weight	87937.0 kDa
excluded_volume	108920 Å³
envelope_volume	144050 Å³
shell_volume	36067 Å³
envelope_diameter	136.4 Å
shell_rg	38.48 Å
envelope_rg	36.64 Å
shape_rg	36.21 Å
total_rg	36.50 Å
total_atoms	6207
n_residues	788
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

▼

3. P(r) Analysis (GNOM)

dmax	125.2 Å
rg_real	36.33 Å
rg_real_error	1.31 Å
i0_real	1.2650e+08
i0_real_error	2.2150e+06
rg_reciprocal	36.06 Å
i0_reciprocal	126400000.0000
total_estimate	0.8002
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.1 Å
skewness	0.633
kurtosis	-0.158
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	12100000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.695; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.685; Smooth: 0.629

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	WIM8E5 Fab Heavy Chain
formula_weight	24512.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	6207

EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPEKGLEWVSGISWNSGTIAYADSVKGRFTISRDNAKNSLYLQMNSLRTEDTAFYYCAKAYGVSGAYFTSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVHHHHHHHHHH

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	WIM8E5 Fab Light Chain
formula_weight	24131.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRISGSGSGTDFTLTISSLQADDVAIYYCQQYDSSPPTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Peptide SVNLNVIVK
formula_weight	986.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

SVNLNVIVK

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	MHC class I antigen
formula_weight	38460.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSLTACKV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 polymer

description	Beta-2-microglobulin
formula_weight	13732.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MSRSVALAVLALLSLSGLEAIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

▶

6. Citations (1)

▶

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	3.23 Å
resolution_method	—
num_particles	92546

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

Cryo-EM structure of the WIM8E5 Fab - HLA-A*11:01 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)