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2rkj

Cocrystal structure of a tyrosyl-tRNA synthetase splicing factor with a group I intron RNA

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tyrosyl-tRNA synthetase

Neurospora crassa

UniProt P12063

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Homooligomer Protein 2 RNA 2 RNA (238-MER) × 1 ;RNA (5'-R(P*GP*CP*UP*U)-3') ; × 1 Consistent with all polymers
2 Protein–RNA Homooligomer Protein 2 RNA 2 RNA (238-MER) × 1 ;RNA (5'-R(P*GP*CP*UP*U)-3') ; × 1 Consistent with all polymers
3 Protein–RNA Homooligomer Protein 2 RNA 2 RNA (238-MER) × 1 ;RNA (5'-R(P*GP*CP*UP*U)-3') ; × 1 Consistent with all polymers
4 Protein–RNA Homooligomer Protein 2 RNA 2 RNA (238-MER) × 1 ;RNA (5'-R(P*GP*CP*UP*U)-3') ; × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1y42 4ojm

2 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2rkj 2rkj 2rkj 2rkj

4 assemblies

View Construct and Data Evidence
UniProt name SYYM_NEUCR
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 2–392； UniProt 33–423 Author chain B； PDBConstruct 2–392； UniProt 33–423 Author chain E； PDBConstruct 2–392； UniProt 33–423 Author chain F； PDBConstruct 2–392； UniProt 33–423 Author chain I； PDBConstruct 2–392； UniProt 33–423 Author chain J； PDBConstruct 2–392； UniProt 33–423 Author chain M； PDBConstruct 2–392； UniProt 33–423 Author chain N； PDBConstruct 2–392； UniProt 33–423

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_id2rkj
Deposition date deposition_date2007-10-16
Structure title titleCocrystal structure of a tyrosyl-tRNA synthetase splicing factor with a group I intron RNA
Keywords keywords;RNA-protein complex, group I intron splicing factor, Aminoacyl-tRNA synthetase, ATP-binding, Ligase, Mitochondrion, mRNA processing, Nucleotide-binding, Protein biosynthesis, Transit peptide, Ligase-RNA COMPLEX ;; Ligase/RNA
Experimental Method methodX-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.

2rkj__assembly_2__model_1

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

Download this curve (.dat)

2rkj__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2rkj__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）37.92 Å
Rg (electron density)38.42 Å
Total Rg38.72 Å
Atom count11082
Residues976
Excluded volume177920 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2rkj__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2rkj__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2rkj__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 2rkj__assembly_4__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)

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7. Citations (1)