3p1z

Crystal structure of the Aperopyrum pernix RNA splicing endonuclease

Method: X-RAY DIFFRACTION

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

Putative uncharacterized protein

Aeropyrum pernix

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	tRNA-splicing endonuclease × 2 （Q9YBF1） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	tRNA-splicing endonuclease × 2 （Q9YBF1） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	tRNA-splicing endonuclease × 2 （Q9YBF1） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9YE85_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–170； UniProt 1–170 Author chain C； PDBConstruct 1–170； UniProt 1–170 Author chain E； PDBConstruct 1–170； UniProt 1–170 Author chain G； PDBConstruct 1–170； UniProt 1–170 Author chain I； PDBConstruct 1–170； UniProt 1–170 Author chain K； PDBConstruct 1–170； UniProt 1–170

tRNA-splicing endonuclease

Aeropyrum pernix

UniProt Q9YBF1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Putative uncharacterized protein × 2 （Q9YE85） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Putative uncharacterized protein × 2 （Q9YE85） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Putative uncharacterized protein × 2 （Q9YE85） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENDA_AERPE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–186； UniProt 1–186 Author chain D； PDBConstruct 1–186； UniProt 1–186 Author chain F； PDBConstruct 1–186； UniProt 1–186 Author chain H； PDBConstruct 1–186； UniProt 1–186 Author chain J； PDBConstruct 1–186； UniProt 1–186 Author chain L； PDBConstruct 1–186； UniProt 1–186

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	3p1z
Deposition date deposition_date	2010-10-01
Structure title title	Crystal structure of the Aperopyrum pernix RNA splicing endonuclease
Keywords keywords	mixed antiparallel and parallel beta-sheet, heterotetramer, RNA splicing, RNA, Splicing endonuclease, HYDROLASE; HYDROLASE
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.

3p1z__assembly_2__model_1

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

Download this curve (.dat)

3p1z__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3p1z__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.01 Å
Rg (electron density)	30.21 Å
Total Rg	30.93 Å
Atom count	5391
Residues	693
Excluded volume	96071 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3p1z__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3p1z__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3p1z__assembly_3__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	Putative uncharacterized protein
Molecular weight formula_weight	18599.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	16581

MGKGEGEVAGCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ

Source Source

Source organism organism	Aeropyrum pernix
NCBI taxonomy ID ncbi_taxonomy_id	56636
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	tRNA-splicing endonuclease
Molecular weight formula_weight	20628.6 kDa
EC 编号 ec_number	3.1.27.9
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

MGDRCAPIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP

Source Source

Source organism organism	Aeropyrum pernix
NCBI taxonomy ID ncbi_taxonomy_id	56636
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	408

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	3p1zA01
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	3p1zA02
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	3p1zB01
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	3p1zB02
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	3p1zC01
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	3p1zC02
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	3p1zD01
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	3p1zD02
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	3p1zE01
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	3p1zE02
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	3p1zF01
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	3p1zF02
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	3p1zG01
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	3p1zG02
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	3p1zH01
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	3p1zH02
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	3p1zI01
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	3p1zI02
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	3p1zJ01
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	3p1zJ02
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	3p1zK01
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	3p1zK02
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	3p1zL01
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	3p1zL02
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 —

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Unit-cell length a length_a	135.036 Å
Unit-cell length b length_b	135.036 Å
Unit-cell length c length_c	156.246 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	18

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	41.239 Å
R factor r_factor	0.2632
R_work r_work	0.2602
R_free r_free	0.3182

Crystal structure of the Aperopyrum pernix RNA splicing endonuclease

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

Putative uncharacterized protein

State in the Current Structure

Other States of the Same Protein in the Database

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

3p1z__assembly_2__model_1

3p1z__assembly_2__model_1 | I(q)

3p1z__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of the Aperopyrum pernix RNA splicing endonuclease

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

Putative uncharacterized protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

3p1z__assembly_2__model_1

3p1z__assembly_2__model_1 | I(q)

3p1z__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)