9w2k

Structural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2)

Method: X-RAY DIFFRACTION

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

tRNA intron endonuclease

Candidatus Micrarchaeum acidiphilum ARMAN-2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 2 RNA 3	;DNA/RNA (5'-R(PAPCPCPGPAPCPCPA)-D(PU)-R(PAPGPCPU)-3') ; × 1 ;RNA (5'-R(PAPGPCPGPGPUPCPA)-3') ; × 1 ;RNA (5'-R(APGPGP*U)-3') ; × 1 ACETIC ACID × 4 ;ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE ; × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C7DIA5_MICA2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–387； UniProt 1–387 Author chain B； PDBConstruct 1–387； UniProt 1–387

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	9w2k
Deposition date deposition_date	2025-07-28
Last revision last_revision	2025-09-10
Structure title title	Structural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2)
Keywords keywords	Archaea, tRNA, Intron, Novel catalytic reaction, SPLICING, SPLICING-RNA complex; SPLICING/RNA
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.

9w2k__assembly_1__model_1

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

Download this curve (.dat)

9w2k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9w2k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.07 Å
Rg (electron density)	29.59 Å
Total Rg	30.37 Å
Atom count	6860
Residues	795
Excluded volume	120930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9w2k__assembly_1__model_1`	pentameric （5）	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 (7)

Entity 1 Entity 1 polymer

Description description	tRNA intron endonuclease
Molecular weight formula_weight	45882.7 kDa
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	7209

MTLLLNINTKAKRISVSDQSTIDILRNGYFGEYRAGKLMLEVEEGLYLVDVRKAACTDENSKPVSFNDIAGVFIKRKKLMARYFTFKDWRDRGLIIKSPGLRFGEEEHVQAKRYPSSAINLKKYSVTGIFFPDDMVTVIDDDESGKDLYENFWLGQYGTYKVSEHGNLNKLDIYETLFLIDMGVISIKNFTRAQIVNIASARRTDIMKLYDVYKDWRTKGYVVKTGFKFGTNFRIYFPGAKPIKENNEWIHSKHVLHVFPRDSKLIISEWARAIRVAHSVRKTFILAIPGKTRKKKLAIDFELYHRRGGDIEIPGKNSPRFGMLSLSENERIGGSELSAIINEAKSRKLELVIAIADSETSVTYYKVRRVDLPKSEYEYYEIDWMQPLEHHHHHH

Source Source

Source organism organism	Candidatus Micrarchaeum acidiphilum ARMAN-2
NCBI taxonomy ID ncbi_taxonomy_id	425595
Host organism host_organism	Escherichia

Entity 2 Entity 2 polymer

Description description	;DNA/RNA (5'-R(PAPCPCPGPAPCPCPA)-D(PU)-R(PAPGPCP*U)-3') ;
Molecular weight formula_weight	4084.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I

ACCGACCAUAGCU

Entity 3 Entity 3 polymer

Description description	;RNA (5'-R(PAPGPCPGPGPUPCPA)-3') ;
Molecular weight formula_weight	2565.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	F

AGCGGUCA

Entity 4 Entity 4 polymer

Description description	;RNA (5'-R(APGPGPU)-3') ;
Molecular weight formula_weight	1280.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	H

AGGU

Entity 5 Entity 5 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	;ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE ;
Molecular weight formula_weight	409.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	349

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Unit-cell length a length_a	53.514 Å
Unit-cell length b length_b	65.648 Å
Unit-cell length c length_c	71.802 Å
Unit-cell angle α angle_alpha	114.46 °
Unit-cell angle β angle_beta	111.89 °
Unit-cell angle γ angle_gamma	90.01 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.798 Å
Low-resolution limit resolution_low	33.529 Å
R factor r_factor	—
R_work r_work	0.1853
R_free r_free	0.2310

Structural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2)

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

tRNA intron endonuclease

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

9w2k__assembly_1__model_1

9w2k__assembly_1__model_1 | I(q)

9w2k__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Structural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2)

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

tRNA intron endonuclease

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

9w2k__assembly_1__model_1

9w2k__assembly_1__model_1 | I(q)

9w2k__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)