2gjw

RNA Recognition and Cleavage by an Splicing Endonuclease

Method: X-RAY DIFFRACTION

▼

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

tRNA-splicing endonuclease

Archaeoglobus fulgidus

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	5'-R(GPCPGPAPCPCPGPAPCPCPAP(DU)PAPGPCPUPGPCPA)-3' × 1 5'-R(UPGPCPAPGPCPGPGPUPCPAP(A23))-3' × 1 5'-R(APGPGPUPCPGPC)-3' × 1	Consistent with all polymers
2	Protein–RNA	Homooligomer	Protein 2 RNA 3	5'-R(GPCPGPAPCPCPGPAPCPCPAP(DU)PAPGPCPUPGPCPA)-3' × 1 5'-R(UPGPCPAPGPCPGPGPUPCPAP(A23))-3' × 1 5'-R(APGPGPUPCPGPC)-3' × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENDA_ARCFU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 10–313； UniProt 2–305 Author chain B； PDBConstruct 10–313； UniProt 2–305 Author chain C； PDBConstruct 10–313； UniProt 2–305 Author chain D； PDBConstruct 10–313； UniProt 2–305

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2gjw
Deposition date deposition_date	2006-03-31
Structure title title	RNA Recognition and Cleavage by an Splicing Endonuclease
Keywords keywords	Bulge-Helix-Bulge RNA-protein complex, Splicing Endonuclease Af, Hydrolase-RNA COMPLEX; Hydrolase/RNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2gjw__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2gjw__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gjw__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.98 Å
Rg (electron density)	28.89 Å
Total Rg	29.47 Å
Atom count	5895
Residues	647
Excluded volume	102380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gjw__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2gjw__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	5'-R(GPCPGPAPCPCPGPAPCPCPAP(DU)PAPGPCPUPGPCP*A)-3'
Molecular weight formula_weight	6059.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E,I
Atom count atom_count	11778

GCGACCGACCAUAGCUGCA

Entity 2 Entity 2 polymer

Description description	5'-R(UPGPCPAPGPCPGPGPUPCPAP(A23))-3'
Molecular weight formula_weight	3913.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	F,J

UGCAGCGGUCAA

Entity 3 Entity 3 polymer

Description description	5'-R(APGPGPUPCPGP*C)-3'
Molecular weight formula_weight	2236.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	H,L

AGGUCGC

Entity 4 Entity 4 polymer

Description description	tRNA-splicing endonuclease
Molecular weight formula_weight	37105.4 kDa
EC 编号 ec_number	3.1.27.9
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D

MHHHHHHHHIGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli

▼

6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (19 domains)

Domain ID domain_id	d2gjwa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d2gjwa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d2gjwa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

Domain ID domain_id	d2gjwa4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

Domain ID domain_id	d2gjwa5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2gjwb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d2gjwb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d2gjwb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

Domain ID domain_id	d2gjwb4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

Domain ID domain_id	d2gjwb5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2gjwc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d2gjwc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d2gjwc3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

Domain ID domain_id	d2gjwc4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

Domain ID domain_id	d2gjwc5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2gjwd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d2gjwd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d2gjwd3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

Domain ID domain_id	d2gjwd4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

CATH v4.4 (12 domains)

Domain ID domain_id	2gjwA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	2gjwA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

Domain ID domain_id	2gjwA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2gjwB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	2gjwB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

Domain ID domain_id	2gjwB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2gjwC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	2gjwC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

Domain ID domain_id	2gjwC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2gjwD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	2gjwD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

Domain ID domain_id	2gjwD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	90.073 Å
Unit-cell length b length_b	140.357 Å
Unit-cell length c length_c	82.048 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	35.090 Å
R factor r_factor	0.2499
R_work r_work	0.2474
R_free r_free	0.2965

RNA Recognition and Cleavage by an Splicing Endonuclease

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

tRNA-splicing 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

2gjw__assembly_2__model_1

2gjw__assembly_2__model_1 | I(q)

2gjw__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (19 domains)

CATH v4.4 (12 domains)

7. Citations (1)

RNA Recognition and Cleavage by an Splicing Endonuclease

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

tRNA-splicing 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

2gjw__assembly_2__model_1

2gjw__assembly_2__model_1 | I(q)

2gjw__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (19 domains)

CATH v4.4 (12 domains)

7. Citations (1)