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8p7b

CryoEM structure of METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry

Method: ELECTRON MICROSCOPY Dmax: 149.8 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 Heteromer Protein × 3 RNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts Chain B； UniProt 1–514 Chain D； UniProt 1–514 Not recorded tRNA N(3)-methylcytidine methyltransferase METTL6 × 1 （Q8TCB7） Serine tRNA × 1 Serine tRNA × 1 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

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 8P7B 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 ligand/ion Different experimental method 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
4RQF human Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec Deposited 2014-11-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 1–514（514 aa）
Chain B 1–514（514 aa）
Mutation：E447K Mutation：E447K 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
8P7C CryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry Deposited 2023-05-30 Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 1
Chains and sequence ranges Author chain B； PDBConstruct 1–514； UniProt 1–514 Author chain D； PDBConstruct 1–514； UniProt 1–514

tRNA N(3)-methylcytidine methyltransferase METTL6

Homo sapiens

UniProt Q8TCB7

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 Heteromer Protein × 3 RNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts Chain A； UniProt 1–284 Not recorded Serine--tRNA ligase, cytoplasmic × 2 （P49591） Serine tRNA × 1 Serine tRNA × 1 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

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 8P7B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7EZG The structure of the human METTL6 enzyme in complex with SAH Deposited 2021-06-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；298 K；PEGRX F7?25% PEG1500?0.1M BIS-Tris pH9.0?0.1M NaCl
Resolution 1.90 Å R-free 0.201
7F1E Structure of METTL6 bound with SAM Deposited 2021-06-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Sodium acetate pH5.2, 2.0M sodium formate
Resolution 2.59 Å R-free 0.227
7F1E Structure of METTL6 bound with SAM Deposited 2021-06-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–284（284 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Sodium acetate pH5.2, 2.0M sodium formate
Resolution 2.59 Å R-free 0.227
8OWX Crystal Structure of METTL6 bound to SAH Deposited 2023-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–271（271 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.1 M BisTRIS propane pH 6.5, 0.2 M sodium sulfate, 20 % PEG3350
Resolution 2.60 Å R-free 0.250
8OWX Crystal Structure of METTL6 bound to SAH Deposited 2023-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–271（271 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.1 M BisTRIS propane pH 6.5, 0.2 M sodium sulfate, 20 % PEG3350
Resolution 2.60 Å R-free 0.250
8OWY Crystal structure of METTL6 mutant 40-269 bound to SAH Deposited 2023-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–269（230 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M BisTRIS, 0.2 M ammonium sulfate and 25% PEG3350
Resolution 3.20 Å R-free 0.300
8OWY Crystal structure of METTL6 mutant 40-269 bound to SAH Deposited 2023-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 40–269（230 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M BisTRIS, 0.2 M ammonium sulfate and 25% PEG3350
Resolution 3.20 Å R-free 0.300
8P7C CryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry Deposited 2023-05-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–284（284 aa）
Chain C 1–284（284 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain A 1–284（284 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

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name METL6_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–284； UniProt 1–284

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 8p7b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8p7b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8p7b
Deposition date deposition_date2023-05-30
Structure title titleCryoEM structure of METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry
Keywords keywordsMETTL6, tRNA, SerRS, Serine tRNA, 3-Methylcytosine, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier42.61 Å
Radius of gyration Rg (electron density) rg_electron42.62 Å
Forward intensity I(0) i0687518000.00
Molecular weight molecular_weight178820.0 kDa
Excluded volume excluded_volume208320 ų
Envelope volume envelope_volume290680 ų
Hydration-shell volume shell_volume59754 ų
Envelope diameter envelope_diameter159.3 Å
Shell Rg shell_rg44.79 Å
Envelope Rg envelope_rg42.36 Å
Shape Rg shape_rg42.59 Å
Total Rg total_rg42.77 Å
Total atoms total_atoms12361
Residues n_residues1261
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 dmax149.8 Å
Rg (real space) rg_real42.90 Å
Rg uncertainty (real space) rg_real_error1.27 Å
I(0) (real space) i0_real6.8750e+08
I(0) uncertainty (real space) i0_real_error1.2720e+07
Rg (reciprocal space) rg_reciprocal42.61 Å
I(0) (reciprocal space) i0_reciprocal687300000.0000
Solution quality estimate total_estimate0.8380
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.5 Å
Skewness Skewness skewness0.572
Kurtosis Kurtosis kurtosis-0.039
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha50700000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.664
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)