SAXSdb — 9yxv

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1. Structure Basics

entry_id	9yxv
deposition_date	2025-10-27
title	Cryo-EM structure of the core region of cIL-U1A-Fab1R-PGA1-sfFab quaternary complex at 2.9 A resolution
keywords	antibody, Fab, RNA, ribozyme, U1A, ribonucleoprotein (snRNP) complex, 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	32.89 Å
rg_electron	32.03 Å
i0	144181000.00
molecular_weight	93188.0 kDa
excluded_volume	115470 Å³
envelope_volume	148730 Å³
shell_volume	39661 Å³
envelope_diameter	115.4 Å
shell_rg	38.03 Å
envelope_rg	31.81 Å
shape_rg	31.95 Å
total_rg	32.79 Å
total_atoms	6554
n_residues	800
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	107.9 Å
rg_real	32.94 Å
rg_real_error	0.77 Å
i0_real	1.4420e+08
i0_real_error	2.4010e+06
rg_reciprocal	32.92 Å
i0_reciprocal	144200000.0000
total_estimate	0.8914
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	38.2 Å
skewness	0.349
kurtosis	-0.419
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	20390000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.884

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	U1 small nuclear ribonucleoprotein A
formula_weight	11209.1 kDa
mutation	Y31H, Q36R
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6554

AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Hairpin II of the U1 snRNA (U1hpII)
formula_weight	5684.4 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

ACCCAUUGCACUCCGGGU

Entity 3 polymer

description	Protein G
formula_weight	7359.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

TPAVTTYKLVINGRTLSGYTTTTAVDAATAEKVFKQYAYVHEVDGEWTYDDATKTFTVTEKPEKLGG

Source

organism	;Streptococcus sp. 'group G' ;
ncbi_taxonomy_id	1320
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	sfFab18 light chain
formula_weight	26082.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

IMKKNIAFLLASMFVFSIATNAYASDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQTMTYPITFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

description	sfFab18 heavy chain
formula_weight	27725.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MKKNIAFLLASMFVFSIATNAYAEISEVQLVESGGGLVQPGGSLRLSCAASGFNFASASIHWVRQAPGKGLEWVASIYSYSGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARNYDYPYWYSEEAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

description	Fab1R heavy chain
formula_weight	28280.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

GDFMKKNIAFLLASMFVFSIATNAYAEISEVQLVESGGGLVQPGGSLRLSCAASGFNIYSSSIHWVRQAPGKGLEWVASIYPYSGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSPWGWFWQYGQYSVALDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 7 polymer

description	Fab1R light chain
formula_weight	23775.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

AQPAMASDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSFYPITFGQGTKVEIKRTVAAPSVFIFPPSDLRTGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 8 non-polymer

description	DECYL-BETA-D-MALTOPYRANOSIDE
formula_weight	482.6 kDa
src_method	syn
entity_count	1

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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	2.90 Å
resolution_method	—
num_particles	430597

fit	/app/data/saxs_computation/yx/9yxv/9yxv.fit
pddf	/app/data/pr_computation/yx/9yxv/9yxv.pr.out
profile	/app/data/saxs_computation/yx/9yxv/9yxv.dat

Cryo-EM structure of the core region of cIL-U1A-Fab1R-PGA1-sfFab quaternary complex at 2.9 A resolution

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)