8tg4

tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with ADP-ribose-2"-phosphate and 2'-OH RNA

Method: X-RAY DIFFRACTION

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

;Probable RNA 2'-phosphotransferase ;

Aeropyrum pernix

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	;RNA (5'-R(UPGPUPA)-3') ; × 1 NITRATE ION × 1 1,2-ETHANEDIOL × 1 ;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3R,4R,5R)-3,5-dihydroxy-4-(phosphonooxy)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name) ; × 1 POTASSIUM ION × 4 CHLORIDE ION × 2 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KPTA_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–206； UniProt 35–220

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	8tg4
Deposition date deposition_date	2023-07-12
Structure title title	tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with ADP-ribose-2"-phosphate and 2'-OH RNA
Keywords keywords	;tRNA 2'-PHOSPHOTRANSFERASE, TPT1, tRNA SPLICING, ADP-ribose-2"-phosphate, Aeropyrum pernix, TRANSFERASE ;; TRANSFERASE
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.

8tg4__assembly_1__model_1

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

Download this curve (.dat)

8tg4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8tg4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.84 Å
Rg (electron density)	17.18 Å
Total Rg	17.94 Å
Atom count	1565
Residues	186
Excluded volume	27692 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8tg4__assembly_1__model_1`	dimeric （2）	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 (8)

Entity 1 Entity 1 polymer

Description description	;Probable RNA 2'-phosphotransferase ;
Molecular weight formula_weight	23382.0 kDa
EC 编号 ec_number	2.7.1.-
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	1718

MGSSHHHHHHSSGLVPRGSHMRVRLSKTLAGILRHHPGRYGVRLTREGWARVSEVVEGLRKAGWSWVEEWHIVGVALHDPKGRYELRNGEIRARYGHSIPVNVEPLPGEPPPILYHGTTEEALPLIMERGIMRGRRLKVHLTSSLEDAVSTGRRHGNLVAVLLVDVECLRRRGLKVERMSKTVYTVDWVPPECIAEVRRESLGRSL

Source Source

Source organism organism	Aeropyrum pernix
NCBI taxonomy ID ncbi_taxonomy_id	56636
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(UPGPUPA)-3') ;
Molecular weight formula_weight	1548.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

UGUAU

Entity 3 Entity 3 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 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 5 Entity 5 non-polymer

Description description	;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3R,4R,5R)-3,5-dihydroxy-4-(phosphonooxy)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name) ;
Molecular weight formula_weight	639.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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Unit-cell length a length_a	39.844 Å
Unit-cell length b length_b	55.701 Å
Unit-cell length c length_c	42.249 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.370 Å
Low-resolution limit resolution_low	41.860 Å
R factor r_factor	0.1499
R_work r_work	0.1486
R_free r_free	0.1750

tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with ADP-ribose-2"-phosphate and 2'-OH RNA

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

;Probable RNA 2'-phosphotransferase ;

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

8tg4__assembly_1__model_1

8tg4__assembly_1__model_1 | I(q)

8tg4__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with ADP-ribose-2"-phosphate and 2'-OH RNA

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

;Probable RNA 2'-phosphotransferase ;

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

8tg4__assembly_1__model_1

8tg4__assembly_1__model_1 | I(q)

8tg4__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)