9nyb

Crystal structure of the pre-reactive state of porcine OAS1 in complex with dsRNA, two ApCpp substrate analogs, three catalytic Mn2+ ions.

Method: X-RAY DIFFRACTION

▼

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

;2'-5'-oligoadenylate synthase 1 ;

Sus scrofa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 2	;RNA (5'-R(GPGPCPUPUPUPUPGPAPCPCPUPUPUPAPUPGPAPA)-3') ; × 1 ;RNA (5'-R(UPUPCPAPUPAPAPAPGPGPUPCPAPAPAPAPGPCPC)-3') ; × 1 DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MANGANESE (II) ION × 6 1,2-ETHANEDIOL × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OAS1_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–349； UniProt 1–349

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	9nyb
Deposition date deposition_date	2025-03-27
Structure title title	Crystal structure of the pre-reactive state of porcine OAS1 in complex with dsRNA, two ApCpp substrate analogs, three catalytic Mn2+ ions.
Keywords keywords	;Innate immunity, bimetallic nucleotidyltransferases, third metal ion in catalysis, manganese effects, TRANSFERASE, TRANSFERASE-RNA complex ;; TRANSFERASE/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.

9nyb__assembly_1__model_1

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

Download this curve (.dat)

9nyb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9nyb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.23 Å
Rg (electron density)	22.20 Å
Total Rg	23.00 Å
Atom count	3705
Residues	387
Excluded volume	63054 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9nyb__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	;2'-5'-oligoadenylate synthase 1 ;
Molecular weight formula_weight	41278.3 kDa
EC 编号 ec_number	2.7.7.84
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	4607

MELRHTPARDLDKFIEDHLLPNTCFRTQVKEAIDIVCRFLKERCFQGTADPVRVSKVVKGGSSGKGTTLRGRSDADLVVFLTKLTSFEDQLRRRGEFIQEIRRQLEACQREQKFKVTFEVQSPRRENPRALSFVLSSPQLQQEVEFDVLPAFDALGQWTPGYKPNPEIYVQLIKECKSRGKEGEFSTCFTELQRDFLRNRPTKLKSLIRLVKHWYQTCKKTHGNKLPPQYALELLTVYAWEQGSRKTDFSTAQGFQTVLELVLKHQKLCIFWEAYYDFTNPVVGRCMLQQLKKPRPVILDPADPTGNVGGGDTHSWQRLAQEARVWLGYPCCKNLDGSLVGAWTMLQKIGSHHHHHH

Source Source

Source organism organism	Sus scrofa
Common name common_name	pig
NCBI taxonomy ID ncbi_taxonomy_id	9823
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(GPGPCPUPUPUPUPGPAPCPCPUPUPUPAPUPGPAP*A)-3') ;
Molecular weight formula_weight	6017.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

GGCUUUUGACCUUUAUGAA

Entity 3 Entity 3 polymer

Description description	;RNA (5'-R(UPUPCPAPUPAPAPAPGPGPUPCPAPAPAPAPGPCP*C)-3') ;
Molecular weight formula_weight	6069.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

UUCAUAAAGGUCAAAAGCC

Entity 4 Entity 4 non-polymer

Description description	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 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 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	874

▶

Unit-cell length a length_a	72.030 Å
Unit-cell length b length_b	72.030 Å
Unit-cell length c length_c	206.320 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	45.712 Å
R factor r_factor	—
R_work r_work	0.1525
R_free r_free	0.2114

Crystal structure of the pre-reactive state of porcine OAS1 in complex with dsRNA, two ApCpp substrate analogs, three catalytic Mn2+ ions.

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

;2'-5'-oligoadenylate synthase 1 ;

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

9nyb__assembly_1__model_1

9nyb__assembly_1__model_1 | I(q)

9nyb__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal structure of the pre-reactive state of porcine OAS1 in complex with dsRNA, two ApCpp substrate analogs, three catalytic Mn2+ ions.

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

;2'-5'-oligoadenylate synthase 1 ;

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

9nyb__assembly_1__model_1

9nyb__assembly_1__model_1 | I(q)

9nyb__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)