SAXSdb — 7f1e

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

tRNA N(3)-methylcytidine methyltransferase METTL6

Homo sapiens

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 1–284	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–284	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

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 7F1E	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 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	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
8OWX Crystal Structure of METTL6 bound to SAH Deposited 2023-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–271（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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 3–286； UniProt 1–284 Author chain B； PDBConstruct 3–286； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7f1e
Deposition date deposition_date	2021-06-09
Structure title title	Structure of METTL6 bound with SAM
Keywords keywords	RNA methyltransferase, RNA, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.31 Å
Radius of gyration Rg (electron density) rg_electron	26.47 Å
Forward intensity I(0) i0	47294900.00
Molecular weight molecular_weight	54291.0 kDa
Excluded volume excluded_volume	68041 Å³
Envelope volume envelope_volume	83269 Å³
Hydration-shell volume shell_volume	26401 Å³
Envelope diameter envelope_diameter	94.4 Å
Shell Rg shell_rg	33.54 Å
Envelope Rg envelope_rg	26.43 Å
Shape Rg shape_rg	26.48 Å
Total Rg total_rg	27.21 Å
Total atoms total_atoms	3827
Residues n_residues	474
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	90.9 Å
Rg (real space) rg_real	27.37 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	4.7290e+07
I(0) uncertainty (real space) i0_real_error	7.0350e+05
Rg (reciprocal space) rg_reciprocal	27.35 Å
I(0) (reciprocal space) i0_reciprocal	47290000.0000
Solution quality estimate total_estimate	0.8844
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.353
Kurtosis Kurtosis kurtosis	-0.511
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7435000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.941

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	tRNA N(3)-methylcytidine methyltransferase METTL6
Molecular weight formula_weight	33491.2 kDa
EC 编号 ec_number	2.1.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3883

GHMASLQRKGLQARILTSEEEEKLKRDQTLVSDFKQQKLEQEAQKNWDLFYKRNSTNFFKDRHWTTREFEELRSCREFEDQKLTMLEAGCGVGNCLFPLLEEDPNIFAYACDFSPRAIEYVKQNPLYDTERCKVFQCDLTKDDLLDHVPPESVDVVMLIFVLSAVHPDKMHLVLQNIYKVLKPGKSVLFRDYGLYDHAMLRFKASSKLGENFYVRQDGTRSYFFTDDFLAQLFMDTGYEEVVNEYVFRETVNKKEGLCVPRVFLQSKFLKPPKNPSPVVLGLDPKS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

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8. Citations (1)

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Unit-cell length a length_a	83.457 Å
Unit-cell length b length_b	83.457 Å
Unit-cell length c length_c	129.686 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
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.589 Å
Low-resolution limit resolution_low	26.857 Å
R factor r_factor	0.1934
R_work r_work	0.1908
R_free r_free	0.2265

fit	/app/data/saxs_computation/f1/7f1e/7f1e.fit
pddf	/app/data/pr_computation/f1/7f1e/7f1e.pr.out
profile	/app/data/saxs_computation/f1/7f1e/7f1e.dat

Structure of METTL6 bound with SAM

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

tRNA N(3)-methylcytidine methyltransferase METTL6

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction