SAXSdb — 4nz6

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 1 TRIETHYLENE GLYCOL × 1 D-LYSINE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	D-GLUTAMIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRUA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–313； UniProt 83–394 Author chain B； PDBConstruct 2–313； UniProt 83–394

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	4nz6
Deposition date deposition_date	2013-12-11
Structure title title	Steroid receptor RNA Activator (SRA) modification by the human Pseudouridine Synthase 1 (hPus1p): RNA binding, activity, and atomic model
Keywords keywords	nuclear receptor coactivator, Steroid receptor RNA Activator, pseudouridylation, nucleus, mitochondrial, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4nz6__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4nz6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4nz6__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.42 Å
Rg (electron density)	20.35 Å
Total Rg	21.12 Å
Atom count	2467
Residues	305
Excluded volume	43938 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4nz6__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4nz6__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	tRNA pseudouridine synthase A, mitochondrial
Molecular weight formula_weight	35670.9 kDa
EC 编号 ec_number	5.4.99.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5470

SKRKIVLLMAYSGKGYHGMQRNVGSSQFKTIEDDLVSALVRSGCIPENHGEDMRKMSFQRCARTDKGVSAAGQVVSLKVWLIDDILEKINSHLPSHIRILGLKRVTGGFNSKNRCDARTYCYLLPTFAFAHKDRDVQDETYRLSAETLQQVNRLLACYKGTHNFHNFTSQKGPQDPSACRYILEMYCEEPFVREGLEFAVIRVKGQSFMMHQIRKMVGLVVAIVKGYAPESVLERSWGTEKVDVPKAPGLGLVLERVHFEKYNQRFGNDGLHEPLDWAQEEGKVAAFKEEHIYPTIIGTERDERSMAQWLSTL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	D-LYSINE
Molecular weight formula_weight	146.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	D-GLUTAMIC ACID
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	477

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4nz6A01
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	4nz6A02
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

Domain ID domain_id	4nz6B01
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	4nz6B02
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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Unit-cell length a length_a	71.420 Å
Unit-cell length b length_b	75.120 Å
Unit-cell length c length_c	110.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.997 Å
R factor r_factor	0.1856
R_work r_work	0.1839
R_free r_free	0.2241

Steroid receptor RNA Activator (SRA) modification by the human Pseudouridine Synthase 1 (hPus1p): RNA binding, activity, and atomic model

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4nz6__assembly_1__model_1

4nz6__assembly_1__model_1 | I(q)

4nz6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Steroid receptor RNA Activator (SRA) modification by the human Pseudouridine Synthase 1 (hPus1p): RNA binding, activity, and atomic model

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4nz6__assembly_1__model_1

4nz6__assembly_1__model_1 | I(q)

4nz6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)