SAXSdb — 6q8j

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1. Protein Identity and Related Structures Protein Identity & Related Structures

WD40 repeat-containing protein SMU1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–196	Not recorded	XS4 1-~{tert}-butyl-3-[6-(3,5-dimethoxyphenyl)-2-[[1-[1-(phenylmethyl)piperidin-4-yl]-1,2,3-triazol-4-yl]methylamino]pyrido[2,3-d]pyrimidin-7-yl]urea × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6, 16-20 % PEG 10K, 0.2 M ammonium acetate	Resolution 1.80 Å R-free 0.220

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6Q8J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5O9Z Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex) Deposited 2017-06-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric	Chain L 1–513（513 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
6AHD The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution Deposited 2018-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric	Chain Y 1–513（513 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6Q8F Nterminal domain of human SMU1 Deposited 2018-12-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–513（512 aa） Chain B 2–513（512 aa）	Not recorded	BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Bis-Tris pH 5.5, 16-20 % PEG 10K, 0.1 M ammonium acetate	Resolution 1.90 Å R-free 0.214
6Q8I Nterminal domain of human SMU1 in complex with human REDmid Deposited 2018-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–513（512 aa） Chain B 2–513（512 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Hepes pH 7.0-7.5, 8-10 % PEG 8K	Resolution 3.17 Å R-free 0.277
6Q8I Nterminal domain of human SMU1 in complex with human REDmid Deposited 2018-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 2–513（512 aa） Chain F 2–513（512 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Hepes pH 7.0-7.5, 8-10 % PEG 8K	Resolution 3.17 Å R-free 0.277
6Q8I Nterminal domain of human SMU1 in complex with human REDmid Deposited 2018-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 2–513（512 aa） Chain J 2–513（512 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Hepes pH 7.0-7.5, 8-10 % PEG 8K	Resolution 3.17 Å R-free 0.277
6Q8I Nterminal domain of human SMU1 in complex with human REDmid Deposited 2018-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain M 2–513（512 aa） Chain N 2–513（512 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Hepes pH 7.0-7.5, 8-10 % PEG 8K	Resolution 3.17 Å R-free 0.277
8H6K Cryo-EM structure of human exon-defined spliceosome in the mature B state. Deposited 2022-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric	Chain 4Z 1–513（513 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8H6L Cryo-EM structure of human exon-defined spliceosome in the early B state. Deposited 2022-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 59-meric	Chain 4Z 1–513（513 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8QO9 Cryo-EM structure of a human spliceosomal B complex protomer Deposited 2023-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 71-meric	Chain v 1–513（513 aa） Chain w 1–513（513 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.29 Å
8QZS Cryo-EM structure of the cross-exon B-like complex Deposited 2023-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 68-meric	Chain v 1–513（513 aa） Chain w 1–513（513 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
9R8V Cryo-EM structure of the human pre-Bact-OTS complex (whole map) Deposited 2025-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 63-meric	Chain v 1–513（513 aa） Chain w 1–513（513 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.50 Å

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SMU1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–197； UniProt 2–196

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6q8j
Deposition date deposition_date	2018-12-14
Structure title title	Nterminal domain of human SMU1 in complex with LSP641
Keywords keywords	Splicing factor, influenza virus, SPLICING; SPLICING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.10 Å
Radius of gyration Rg (electron density) rg_electron	22.95 Å
Forward intensity I(0) i0	8774520.00
Molecular weight molecular_weight	22469.0 kDa
Excluded volume excluded_volume	28379 Å³
Envelope volume envelope_volume	36936 Å³
Hydration-shell volume shell_volume	15399 Å³
Envelope diameter envelope_diameter	87.0 Å
Shell Rg shell_rg	26.51 Å
Envelope Rg envelope_rg	23.53 Å
Shape Rg shape_rg	22.94 Å
Total Rg total_rg	23.52 Å
Total atoms total_atoms	1585
Residues n_residues	188
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	85.4 Å
Rg (real space) rg_real	23.51 Å
Rg uncertainty (real space) rg_real_error	1.30 Å
I(0) (real space) i0_real	8.7750e+06
I(0) uncertainty (real space) i0_real_error	1.5490e+05
Rg (reciprocal space) rg_reciprocal	23.42 Å
I(0) (reciprocal space) i0_reciprocal	8774000.0000
Solution quality estimate total_estimate	0.7589
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.742
Kurtosis Kurtosis kurtosis	0.062
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1136000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.484; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.424; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	WD40 repeat-containing protein SMU1
Molecular weight formula_weight	22115.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1709

MGSIEIESSDVIRLIMQYLKENSLHRALATLQEETTVSLNTVDSIESFVADINSGHWDTVLQAIQSLKLPDKTLIDLYEQVVLELIELRELGAARSLLRQTDPMIMLKQTQPERYIHLENLLARSYFDPREAYPDGSSKEKRRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLPPGMTIDLFRGKAAVKDV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;1-~{tert}-butyl-3-[6-(3,5-dimethoxyphenyl)-2-[[1-[1-(phenylmethyl)piperidin-4-yl]-1,2,3-triazol-4-yl]methylamino]pyrido[2,3-d]pyrimidin-7-yl]urea ;
Molecular weight formula_weight	650.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	102

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8. Citations (1)

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Unit-cell length a length_a	72.193 Å
Unit-cell length b length_b	72.193 Å
Unit-cell length c length_c	183.164 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	43.720 Å
R factor r_factor	0.1636
R_work r_work	0.1606
R_free r_free	0.2201

fit	/app/data/saxs_computation/q8/6q8j/6q8j.fit
pddf	/app/data/pr_computation/q8/6q8j/6q8j.pr.out
profile	/app/data/saxs_computation/q8/6q8j/6q8j.dat

Nterminal domain of human SMU1 in complex with LSP641

1. Protein Identity and Related Structures Protein Identity & Related Structures

WD40 repeat-containing protein SMU1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction