SAXSdb — 4its

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

tRNA pseudouridine synthase A, mitochondrial

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 79–408	Fragment：catalytic domain (unp residues 79-408)	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.1；295 K；18% (w/v) PEG8000, 0.1 M MES, 0.2 M AmSO4 , pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.226
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 79–408	Fragment：catalytic domain (unp residues 79-408)	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.1；295 K；18% (w/v) PEG8000, 0.1 M MES, 0.2 M AmSO4 , pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.226

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 4ITS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4IQM Crystal structure of the catalytic domain of human Pus1 Deposited 2013-01-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–408（330 aa） Fragment：catalytic domain (unp residues 79-408)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；28% w/v PEG4000, 0.2 M magnesium chloride, 0.1 M Tris-HCl pH 8.5, 1 mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.80 Å R-free 0.227
4J37 Crystal structure of the catalytic domain of human Pus1 Deposited 2013-02-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–408（330 aa） Fragment：catalytic domain (unp residues 79-408)	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；295 K；18% PEG8000, 0.1 M MES, 0.3 M AmSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.75 Å R-free 0.239
4NZ6 Steroid receptor RNA Activator (SRA) modification by the human Pseudouridine Synthase 1 (hPus1p): RNA binding, activity, and atomic model Deposited 2013-12-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 83–394（312 aa） Fragment：catalytic domain, UNP residues 83-394	Not recorded	EDO 1,2-ETHANEDIOL × 1 PGE TRIETHYLENE GLYCOL × 1 DLY D-LYSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；28% PEG 3350/glycerol, 0.1M Bicine/TRIS (pH 8.5), 10% amino acids mixture, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.224
4NZ6 Steroid receptor RNA Activator (SRA) modification by the human Pseudouridine Synthase 1 (hPus1p): RNA binding, activity, and atomic model Deposited 2013-12-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 83–394（312 aa） Fragment：catalytic domain, UNP residues 83-394	Not recorded	DGL D-GLUTAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；28% PEG 3350/glycerol, 0.1M Bicine/TRIS (pH 8.5), 10% amino acids mixture, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.224
4NZ7 Steroid receptor RNA Activator (SRA) modification by the human Pseudouridine Synthase 1 (hPus1p): RNA binding, activity, and atomic model Deposited 2013-12-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 83–394（312 aa） Fragment：catalytic domain, UNP residues 83-394	Mutation：D146A	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；17% PEG 8000, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.238
9H51 Assembly intermediate of human mitochondrial ribosome small subunit in complex with PUS1, METTL15 and RBFA(IN conformation) (state M1) Deposited 2024-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric	Chain c 29–412（384 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 1 MG MAGNESIUM ION × 40 K POTASSIUM ION × 6 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRUA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–336； UniProt 79–408

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	4its
Deposition date deposition_date	2013-01-18
Structure title title	Crystal structure of the catalytic domain of human Pus1 with MES in the active site
Keywords keywords	;beta sheet, isomerase, pseudouridine synthase, RNA binding protein, RNA modification, tRNA, pre-tRNA, steroid receptor RNA activator, U2 snRNA ;; RNA BINDING PROTEIN
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	21.56 Å
Radius of gyration Rg (electron density) rg_electron	20.53 Å
Forward intensity I(0) i0	20997600.00
Molecular weight molecular_weight	34221.0 kDa
Excluded volume excluded_volume	42615 Å³
Envelope volume envelope_volume	50054 Å³
Hydration-shell volume shell_volume	20740 Å³
Envelope diameter envelope_diameter	69.9 Å
Shell Rg shell_rg	26.70 Å
Envelope Rg envelope_rg	20.76 Å
Shape Rg shape_rg	20.54 Å
Total Rg total_rg	21.33 Å
Total atoms total_atoms	2410
Residues n_residues	296
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	71.2 Å
Rg (real space) rg_real	21.56 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	2.1000e+07
I(0) uncertainty (real space) i0_real_error	2.7940e+05
Rg (reciprocal space) rg_reciprocal	21.56 Å
I(0) (reciprocal space) i0_reciprocal	21000000.0000
Solution quality estimate total_estimate	0.8822
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.374
Kurtosis Kurtosis kurtosis	-0.314
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5746000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.965

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	tRNA pseudouridine synthase A, mitochondrial
Molecular weight formula_weight	37950.4 kDa
EC 编号 ec_number	5.4.99.12
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	2570

GPGSEFEKPPKRKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTDKGVSAAGQVVSLKVWLIDDILEKINSHLPSHIRILGLKRVTGGFNSKNRCDARTYCYLLPTFAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQDPSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLERSWGTEKVDVPKAPGLGLVLERVHFEKYNQRFGNDGLHEPLDWAQEEGKVAAFKEEHIYPTIIGTERDERSMAQWLSTLPIHNFSATALTAGG

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	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	154

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4itsA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	580 — Pseudouridine synthase I, catalytic domain, N-terminal subdomain

Domain ID domain_id	4itsA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	660 — Pseudouridine synthase I, catalytic domain, C-terminal subdomain

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8. Citations (1)

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Unit-cell length a length_a	51.860 Å
Unit-cell length b length_b	51.860 Å
Unit-cell length c length_c	446.200 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	1.850 Å
Low-resolution limit resolution_low	44.910 Å
R factor r_factor	0.1845
R_work r_work	0.1818
R_free r_free	0.2261

fit	/app/data/saxs_computation/it/4its/4its.fit
pddf	/app/data/pr_computation/it/4its/4its.pr.out
profile	/app/data/saxs_computation/it/4its/4its.dat

Crystal structure of the catalytic domain of human Pus1 with MES in the active site

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

tRNA pseudouridine synthase A, mitochondrial

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