SAXSdb — 8ipk

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

12S rRNA N4-methylcytidine (m4C) methyltransferase

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 70–407	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；42% PEG 600, 0.2 M imidazole malate, pH 5.5	Resolution 1.90 Å R-free 0.221

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 8IPK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7PNX Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation a Deposited 2021-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 32-meric	Chain b 1–407（407 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MG MAGNESIUM ION × 64 K POTASSIUM ION × 16 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å
7PNY Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation b Deposited 2021-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 32-meric	Chain b 1–407（407 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MG MAGNESIUM ION × 61 K POTASSIUM ION × 20 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.06 Å
7PNZ Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation c Deposited 2021-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 32-meric	Chain b 1–407（407 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MG MAGNESIUM ION × 61 K POTASSIUM ION × 17 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
8IPI The apo structure of human mitochondrial methyltransferase METTL15 Deposited 2023-03-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–407（338 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10% PEG MME 2000, 0.2M Ammonium sulfate, 0.1 M sodium acetate (pH 5.5)	Resolution 2.10 Å R-free 0.229
8IPL The structure of human mitochondrial methyltransferase METTL15 with RBFA and SAM Deposited 2023-03-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 70–407（338 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；17% w/v PEG 4000, 0.05M Potassium chloride, 0.1M Lithium chloride, 0.012M Spermine tetrahydrochloride, 0.05M MES PH6.5	Resolution 2.20 Å R-free 0.235
8IPM The structure of human mitochondrial methyltransferase METTL15 with h44_RNA, RBFA and SAM Deposited 2023-03-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain D 70–407（338 aa）	Not recorded	SFG SINEFUNGIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；20% PEG 4000, 0.2 M ADA (pH 6.4)	Resolution 3.10 Å R-free 0.288
8QRL mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 2 Deposited 2023-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 31-meric	Chain 8 1–407（407 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MG MAGNESIUM ION × 64 K POTASSIUM ION × 16 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
9G5C Assembly intermediate of human mitochondrial ribosome small subunit (State B) Deposited 2024-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 32-meric	Chain b 1–407（407 aa）	Not recorded	MG MAGNESIUM ION × 23 K POTASSIUM ION × 4 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20mM HEPES-HCl, 100mM KCl, 20mM MgCl2, 0.02% DDM, 1mM PMSF, 1x protease-inhibitor mix, 0.5mM GMP-PNP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9G5D Assembly intermediate of human mitochondrial ribosome small subunit (State C) Deposited 2024-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 32-meric	Chain b 1–407（407 aa）	Not recorded	MG MAGNESIUM ION × 10 K POTASSIUM ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20mM HEPES-HCl, 100mM KCl, 20mM MgCl2, 0.02% DDM, 1mM PMSF, 1x protease-inhibitor mix, 0.5mM GMP-PNP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9H51 Assembly intermediate of human mitochondrial ribosome small subunit in complex with PUS1, METTL15 and RBFA(IN conformation) (state M1) Deposited 2024-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric	Chain b 1–407（407 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 1 MG MAGNESIUM ION × 40 K POTASSIUM ION × 6 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9IGT Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15, RBFA, and mtIF2 (State M2.1) Deposited 2025-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric	Chain b 1–407（407 aa）	Not recorded	MG MAGNESIUM ION × 12 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.96 Å
9IGU Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15 and RBFA (Inward conformation) (State M2) Deposited 2025-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 32-meric	Chain b 1–407（407 aa）	Not recorded	MG MAGNESIUM ION × 31 FES FE2/S2 (INORGANIC) CLUSTER × 2 ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.64 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MET15_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–338； UniProt 70–407

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	8ipk
Deposition date deposition_date	2023-03-14
Structure title title	The structure of human mitochondrial methyltransferase METTL15 with SAM
Keywords keywords	human mitochondrial methyltransferase METTL15, RIBOSOMAL PROTEIN; RIBOSOMAL PROTEIN
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	20.96 Å
Radius of gyration Rg (electron density) rg_electron	20.21 Å
Forward intensity I(0) i0	20740300.00
Molecular weight molecular_weight	34714.0 kDa
Excluded volume excluded_volume	43638 Å³
Envelope volume envelope_volume	51130 Å³
Hydration-shell volume shell_volume	21296 Å³
Envelope diameter envelope_diameter	70.1 Å
Shell Rg shell_rg	26.80 Å
Envelope Rg envelope_rg	20.50 Å
Shape Rg shape_rg	20.22 Å
Total Rg total_rg	21.12 Å
Total atoms total_atoms	2435
Residues n_residues	311
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	68.3 Å
Rg (real space) rg_real	20.92 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	2.0740e+07
I(0) uncertainty (real space) i0_real_error	2.4220e+05
Rg (reciprocal space) rg_reciprocal	20.93 Å
I(0) (reciprocal space) i0_reciprocal	20740000.0000
Solution quality estimate total_estimate	0.8068
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	67.3 Å
Skewness Skewness skewness	0.346
Kurtosis Kurtosis kurtosis	-0.235
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4612000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	12S rRNA N4-methylcytidine (m4C) methyltransferase
Molecular weight formula_weight	37768.6 kDa
EC 编号 ec_number	2.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2534

KLHIPVMVDEVVHCLSPQKGQIFLDMTFGSGGHTKAILQKESDIVLYALDRDPTAYALAEHLSELYPKQIRAMLGQFSQAEALLMKAGVQPGTFDGVLMDLGCSSMQLDTPERGFSLRKDGPLDMRMDGGRYPDMPTAADVVNALDQQALASILRTYGEEKHAKKIASAIVQARSIYPITRTQQLASIVAGAFPPSAIYTRKDLLQRSTHIATKTFQALRIFVNNELNELYTGLKTAQKFLRPGGRLVALSFHSLEDRIVKRFLLGISMTERFNLSVRQQVMKTSQLGSDHENTEEVSMRRAPLMWELIHKKVLSPQDQDVQDNPRGRSAKLRAAIKL

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

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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8. Citations (1)

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Unit-cell length a length_a	70.506 Å
Unit-cell length b length_b	70.506 Å
Unit-cell length c length_c	134.674 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	25.245 Å
R factor r_factor	0.1842
R_work r_work	0.1823
R_free r_free	0.2207

fit	/app/data/saxs_computation/ip/8ipk/8ipk.fit
pddf	/app/data/pr_computation/ip/8ipk/8ipk.pr.out
profile	/app/data/saxs_computation/ip/8ipk/8ipk.dat

The structure of human mitochondrial methyltransferase METTL15 with SAM

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

12S rRNA N4-methylcytidine (m4C) methyltransferase

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