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4rqf

human Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec

Method: X-RAY DIFFRACTION Dmax: 129.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine--tRNA ligase, cytoplasmic

Homo sapiens

UniProt P49591

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Homooligomer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 1–514 Chain B； UniProt 1–514 Mutation：E447K selenocysteine tRNA × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 SER SERINE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；298 K；18%(m/v) PEG3350, 0.1M NaCl, 0.1M Tris-HCl (pH8.0), 0.1M Sodium malonate pH7.0., VAPOR DIFFUSION, temperature 298K Resolution 3.50 Å R-free 0.314

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4RQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3VBB Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms Deposited 2012-01-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–514（514 aa）
Chain B 1–514（514 aa）
Not recorded MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 3350, 0.2 M tri-sodium citrate pH 7.0, 5mM ATP, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.89 Å R-free 0.250
3VBB Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms Deposited 2012-01-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–514（514 aa）
Chain D 1–514（514 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 3350, 0.2 M tri-sodium citrate pH 7.0, 5mM ATP, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.89 Å R-free 0.250
3VBB Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms Deposited 2012-01-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–514（514 aa）
Chain F 1–514（514 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 3350, 0.2 M tri-sodium citrate pH 7.0, 5mM ATP, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.89 Å R-free 0.250
4L87 Crystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9 Angstrom resolution Deposited 2013-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–477（476 aa） Fragment：UNP residues 2-477
Not recorded SSA 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE × 2 PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG3350, 0.2 M ammonium fluoride or ammonium formate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.90 Å R-free 0.268
4RQE human Seryl-tRNA synthetase dimer complexed with two molecules of tRNAsec Deposited 2014-11-03 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–514（514 aa）
Chain C 1–514（514 aa）
Mutation：E156T, R157S Mutation：E156T, R157S SER SERINE × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；18%(m/v) PEG3350, 0.1M NaCl, 0.1M Tris-HCl (pH8.0), 0.1M Sodium malonate pH7.0. , VAPOR DIFFUSION, temperature 298K
Resolution 4.00 Å R-free 0.322
8P7B CryoEM structure of METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry Deposited 2023-05-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–514（514 aa）
Chain D 1–514（514 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.42 Å
8P7C CryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry Deposited 2023-05-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–514（514 aa）
Chain D 1–514（514 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8P7D CryoEM structure of METTL6 tRNA SerRS complex in a 1:1:2 stoichiometry Deposited 2023-05-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–514（514 aa）
Chain D 1–514（514 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9DPD Cryo-EM structure of SerRS dimer in complex with one SIRT2 Deposited 2024-09-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–514（514 aa）
Chain D 1–514（514 aa）
Not recorded AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.87 Å
9DPI Cryo-EM structure of SerRS dimer in complex with two SIRT2 Deposited 2024-09-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–514（514 aa）
Chain F 1–514（514 aa）
Not recorded AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；in 25mM HEPES-Na pH7.5, 150mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SYSC_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–514； UniProt 1–514 Author chain B； PDBConstruct 1–514； UniProt 1–514

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4rqf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4rqf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4rqf
Deposition date deposition_date2014-11-03
Structure title titlehuman Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec
Keywords keywordsaminoacyl-tRNA synthetase, classII aaRS, aminoacylation, serine, cytosol, LIGASE-RNA complex; LIGASE/RNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.17 Å
Radius of gyration Rg (electron density) rg_electron36.28 Å
Forward intensity I(0) i0301968000.00
Molecular weight molecular_weight123800.0 kDa
Excluded volume excluded_volume147970 ų
Envelope volume envelope_volume211400 ų
Hydration-shell volume shell_volume49619 ų
Envelope diameter envelope_diameter135.5 Å
Shell Rg shell_rg41.45 Å
Envelope Rg envelope_rg36.69 Å
Shape Rg shape_rg36.23 Å
Total Rg total_rg36.75 Å
Total atoms total_atoms8619
Residues n_residues971
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax129.6 Å
Rg (real space) rg_real37.26 Å
Rg uncertainty (real space) rg_real_error1.21 Å
I(0) (real space) i0_real3.0200e+08
I(0) uncertainty (real space) i0_real_error5.4820e+06
Rg (reciprocal space) rg_reciprocal37.21 Å
I(0) (reciprocal space) i0_reciprocal302000000.0000
Solution quality estimate total_estimate0.8693
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.2 Å
Skewness Skewness skewness0.373
Kurtosis Kurtosis kurtosis-0.334
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33450000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.896; Smooth: 0.935
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4rqfA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily40 — Serine-tRNA synthetase, tRNA binding domain
Domain ID domain_id4rqfA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id4rqfB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily40 — Serine-tRNA synthetase, tRNA binding domain
Domain ID domain_id4rqfB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
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8. Citations (1)

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9. Files and Curves (10)