SAXSdb — 9b0e

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

RNA cytidine acetyltransferase

Thermochaetoides thermophila DSM 1495

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–1073 Chain B； UniProt 1–1073	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 A1AH4 [[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[[1-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]amino]-2-oxidanylidene-ethyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.19 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 9B0E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5JPQ Cryo-EM structure of the 90S pre-ribosome Deposited 2016-05-04	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric	Chain i 1–1073（1073 aa） Chain j 1–1073（1073 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.30 Å
5OQL Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum Deposited 2017-08-12	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 55-meric	Chain i 1–1073（1073 aa） Chain j 1–1073（1073 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6RXT Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state A Deposited 2019-06-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 57-meric	Chain CR 1–1073（1073 aa） Chain CS 1–1073（1073 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.00 Å
6RXU Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B1 Deposited 2019-06-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 66-meric	Chain CR 1–1073（1073 aa） Chain CS 1–1073（1073 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6RXV Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B2 Deposited 2019-06-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain CR 1–1073（1073 aa） Chain CS 1–1073（1073 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
6RXX Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state C, Poly-Ala Deposited 2019-06-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain CR 1–1073（1073 aa） Chain CS 1–1073（1073 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.10 Å
6RXY Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state a Deposited 2019-06-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 59-meric	Chain CR 1–1073（1073 aa） Chain CS 1–1073（1073 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
6RXZ Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state b Deposited 2019-06-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain CR 1–1073（1073 aa） Chain CS 1–1073（1073 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
9AYM Cryo-EM Structure of E.coli produced recombinant N-acetyltransferase 10 (NAT10) in complex with cytidine-acetone-CoA bisubstrate probe Deposited 2024-03-08	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–1073（1073 aa） Chain B 1–1073（1073 aa）	Not recorded	A1AHN [[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S})-4-[[3-[2-[3-[1-[(2~{R},3~{R},4~{R},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]sulfanyl-2-oxidanylidene-propyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
9B0I Cryo-EM Structure of Sf9 produced recombinant N-acetyltransferase 10 (NAT10) in complex with cytidine-amide-CoA bisubstrate probe and ADP/Mg2+. Deposited 2024-03-12	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–1073（1073 aa） Chain B 1–1073（1073 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 A1AH4 [[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[[1-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]amino]-2-oxidanylidene-ethyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.02 Å

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

View Construct and Data Evidence

UniProt name	G0S273_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–1086； UniProt 1–1073 Author chain B； PDBConstruct 14–1086； UniProt 1–1073

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	9b0e
Deposition date deposition_date	2024-03-12
最后修订 last_revision	2024-09-11
Structure title title	Cryo-EM Structure of E.coli produced recombinant N-acetyltransferase 10 (NAT10) in complex with cytidine-amide-CoA bisubstrate probe and ADP
Keywords keywords	RNA binding protein, ac4C modification, RNA acetyltransferase; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	42.40 Å
Radius of gyration Rg (electron density) rg_electron	42.13 Å
Forward intensity I(0) i0	497198000.00
Molecular weight molecular_weight	187060.0 kDa
Excluded volume excluded_volume	235910 Å³
Envelope volume envelope_volume	315160 Å³
Hydration-shell volume shell_volume	62013 Å³
Envelope diameter envelope_diameter	145.4 Å
Shell Rg shell_rg	47.62 Å
Envelope Rg envelope_rg	41.61 Å
Shape Rg shape_rg	42.12 Å
Total Rg total_rg	42.44 Å
Total atoms total_atoms	13158
Residues n_residues	1642
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	140.1 Å
Rg (real space) rg_real	42.44 Å
Rg uncertainty (real space) rg_real_error	1.88 Å
I(0) (real space) i0_real	4.9720e+08
I(0) uncertainty (real space) i0_real_error	9.5530e+06
Rg (reciprocal space) rg_reciprocal	42.40 Å
I(0) (reciprocal space) i0_reciprocal	497200000.0000
Solution quality estimate total_estimate	0.8816
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.2 Å
Skewness Skewness skewness	0.351
Kurtosis Kurtosis kurtosis	-0.434
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	117600000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.776

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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	RNA cytidine acetyltransferase
Molecular weight formula_weight	121475.9 kDa
EC 编号 ec_number	2.3.1.-
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	13158

HHHHHHENLYFQGMTVQKTVDSRIPTLIRNGLQTKKRSFFVVVGDHAKEAIVHLYYIMSSMDVRQNKSVLWAYKKELLGFTSHRKKREAKIKKEIKRGIREPNQADPFELFISLNDIRYCYYKETDKILGNTYGMCILQDFEAITPNILARTIETVEGGGLVVLLLKGMTSLKQLYTMTMDVHARYRTEAHDDVIARFNERFLLSLGSCESCLVIDDELNVLPISGGKGVKPLPPPDEDEELSPAAKELKKIKDELEDTQPIGSLIKLARTVDQAKALLTFVDAIAEKTLRNTVTLTAARGRGKSAAMGVAIAAAVAYGYSNIFITSPSPENLKTLFEFVFKGFDALDYKDHADYTIIQSTNPEFNKAIVRVNIHRNHRQTIQYIRPQDAHVLGQAELVVIDEAAAIPLPLVKKLMGPYLVFMASTISGYEGTGRSLSLKLIKQLREQSRAGANPNGGNAVEVDRSTLKATKETTSVGGRSLKEITLSEPIRYAQGDNVEKWLNTLLCLDATLPRSKISTTGCPDPSQCELLHVNRDTLFSFHPVSEKFLQQMVALYVASHYKNSPNDLQLMSDAPAHELFVLTGPIQEGRLPEPLCVIQVSLEGKISKQSILKSLSRGQQPAGDLIPWLVSQQFQDDEFASLSGARIVRIATNPDYMSMGYGSKALQLLVDYYEGKFADLSEDAAAEVPRSIPRVTDAELSKGSLFDDIKVRDMHELPPLFSKLSERRPEKLDYVGVSYGLTQQLHKFWKRAQFVPVYLRQTANDLTGEHTCVMIRPLQDGNDPSWLGAFAADFHKRFLSLLSYKFREFPSILALTIEESANAGAMLDPSNAPTELTKAELDQLFTPFDHKRLESYANGLLDYHVVLDLMPTIAQLYFTGRLREAVKLSGLQQAILLALGLQRKDIDTLATELNLPGSQVLAIFMKIMRKVTQHFGALVSGAIAAELPDPNKTVGVSKENAMGIHDDEVVGLKFEALEQRLEDELDEGGDEALRELRKKQRELIDSLPLDQYEIDGDDDAWKEAEKRVASAAKSGKKVDGTLVSVPSAKAAKRKAEEMAALRDELEKMEKGKERGSKKAKKEKRR

来源 Source

来源生物 organism	Thermochaetoides thermophila DSM 1495
NCBI Class编号 ncbi_taxonomy_id	759272
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	;[[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[[1-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]amino]-2-oxidanylidene-ethyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate ;
Molecular weight formula_weight	1050.8 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.19 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	73181

fit	/app/data/saxs_computation/b0/9b0e/9b0e.fit
pddf	/app/data/pr_computation/b0/9b0e/9b0e.pr.out
profile	/app/data/saxs_computation/b0/9b0e/9b0e.dat

Cryo-EM Structure of E.coli produced recombinant N-acetyltransferase 10 (NAT10) in complex with cytidine-amide-CoA bisubstrate probe and ADP

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

RNA cytidine acetyltransferase

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

冷冻电镜 EM 3D