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8owx

Crystal Structure of METTL6 bound to SAH

Method: X-RAY DIFFRACTION Dmax: 89.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–271 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–271 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

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 8OWX 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 construct 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 construct Different ligand/ion 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 construct Different ligand/ion 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
8OWY Crystal structure of METTL6 mutant 40-269 bound to SAH Deposited 2023-04-28 Different construct 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 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
8P7B CryoEM structure of METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry Deposited 2023-05-30 Different construct 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 A 1–284（284 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 construct 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 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 construct 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 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 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name METL6_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–275； UniProt 1–271 Author chain B； PDBConstruct 5–275； UniProt 1–271

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 8owx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8owx
Deposition date deposition_date2023-04-28
Structure title titleCrystal Structure of METTL6 bound to SAH
Keywords keywordstRNA modification, m3C, methyltransferase, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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_guinier27.24 Å
Radius of gyration Rg (electron density) rg_electron26.53 Å
Forward intensity I(0) i051827200.00
Molecular weight molecular_weight56798.0 kDa
Excluded volume excluded_volume71215 ų
Envelope volume envelope_volume84893 ų
Hydration-shell volume shell_volume26850 ų
Envelope diameter envelope_diameter95.0 Å
Shell Rg shell_rg33.47 Å
Envelope Rg envelope_rg26.47 Å
Shape Rg shape_rg26.51 Å
Total Rg total_rg27.30 Å
Total atoms total_atoms4001
Residues n_residues478
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 dmax89.2 Å
Rg (real space) rg_real27.30 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real5.1830e+07
I(0) uncertainty (real space) i0_real_error7.5950e+05
Rg (reciprocal space) rg_reciprocal27.29 Å
I(0) (reciprocal space) i0_reciprocal51830000.0000
Solution quality estimate total_estimate0.8877
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.7 Å
Skewness Skewness skewness0.357
Kurtosis Kurtosis kurtosis-0.528
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9688000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.954
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)