SAXSdb — 9t6l

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1. Structure Basics

entry_id	9t6l
deposition_date	2025-11-07
title	Cryo-EM structure of the human LENG8-PCID2-DSS1 complex bound to UAP56 and RRP1B
keywords	RNA metabolism, RNA decay, splicing quality control, NUCLEAR PROTEIN; NUCLEAR PROTEIN
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	32.59 Å
rg_electron	31.73 Å
i0	89608000.00
molecular_weight	76695.0 kDa
excluded_volume	96704 Å³
envelope_volume	128750 Å³
shell_volume	34882 Å³
envelope_diameter	104.7 Å
shell_rg	37.51 Å
envelope_rg	31.40 Å
shape_rg	31.72 Å
total_rg	32.29 Å
total_atoms	5400
n_residues	671
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	105.1 Å
rg_real	32.57 Å
rg_real_error	0.97 Å
i0_real	8.9610e+07
i0_real_error	1.5240e+06
rg_reciprocal	32.58 Å
i0_reciprocal	89610000.0000
total_estimate	0.8952
solution_quality	GOOD a GOOD solution
n_peaks	0
r_peak_primary	— Å
skewness	0.240
kurtosis	-0.573
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	20050000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.832

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Spliceosome RNA helicase DDX39B
formula_weight	49412.6 kDa
ec_number	3.6.4.13
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	5400

GPDSMAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIEQTR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Leukocyte receptor cluster member 8,Ribosomal RNA processing protein 1 homolog B
formula_weight	30940.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GPDIVGTCPDITKHYLRLTCAPDPSTVRPVAVLKKSLCMVKCHWKEKQDYAFACEQMKSIRQDLTVQGIRTEFTVEVYETHARIALEKGDHEEFNQCQTQLKSLYAENLPGNVGEFTAYRILYYIFTKNSGDITTELAYLTRELKADPCVAHALALRTAWALGNYHRFFRLYCHAPCMSGYLVDKFADRERKVALKAMIKTFRPALPVSYLQAELAFEGEAACRAFLEPLGLAYTGPDNSSIDCRLSLAQLSAFGSKPLTTTPRRRPRAMDFF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	PCI domain-containing protein 2
formula_weight	46371.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MGSMAHITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPPYDEMFAAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRVFANNADQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLFKIYFKINKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHCHRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	26S proteasome complex subunit SEM1
formula_weight	8284.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAELEKHGYKMETS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

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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	triclinic

resolution	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	892731

fit	/app/data/saxs_computation/t6/9t6l/9t6l.fit
pddf	/app/data/pr_computation/t6/9t6l/9t6l.pr.out
profile	/app/data/saxs_computation/t6/9t6l/9t6l.dat

Cryo-EM structure of the human LENG8-PCID2-DSS1 complex bound to UAP56 and RRP1B

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

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)