SAXSdb — 8dpe

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

ATP-dependent RNA helicase DDX42

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 211–646	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；1 uL 8 mg/mL DDX42 (in 25 mM Tris, pH 7.5, 300 mM sodium chloride, 1 mM TCEP) + 1 uL reservoir solution (6-10% PEG8000, 0.1 M Tris, pH 8.5-9.0)	Resolution 1.53 Å R-free 0.255

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 8DPE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7EVN The cryo-EM structure of the DDX42-SF3b complex Deposited 2021-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–938（938 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8HK1 The cryo-EM structure of human pre-17S U2 snRNP Deposited 2022-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 20 PDB declaration: 21-meric	Chain E 1–938（938 aa）	Not recorded	9B0 [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate × 1 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DDX42_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–444； UniProt 211–646

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	8dpe
Deposition date deposition_date	2022-07-15
Structure title title	Crystal structure of ATP-dependent RNA helicase DDX42
Keywords keywords	DDX42, splicing factor, RNA helicase, SPLICING, HYDROLASE; SPLICING, HYDROLASE
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	26.11 Å
Radius of gyration Rg (electron density) rg_electron	25.29 Å
Forward intensity I(0) i0	41055100.00
Molecular weight molecular_weight	48965.0 kDa
Excluded volume excluded_volume	61208 Å³
Envelope volume envelope_volume	75381 Å³
Hydration-shell volume shell_volume	25797 Å³
Envelope diameter envelope_diameter	87.7 Å
Shell Rg shell_rg	31.67 Å
Envelope Rg envelope_rg	25.31 Å
Shape Rg shape_rg	25.29 Å
Total Rg total_rg	26.05 Å
Total atoms total_atoms	3449
Residues n_residues	436
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	84.2 Å
Rg (real space) rg_real	26.18 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	4.1060e+07
I(0) uncertainty (real space) i0_real_error	5.8020e+05
Rg (reciprocal space) rg_reciprocal	26.16 Å
I(0) (reciprocal space) i0_reciprocal	41050000.0000
Solution quality estimate total_estimate	0.8655
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.412
Kurtosis Kurtosis kurtosis	-0.429
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10450000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.653

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	ATP-dependent RNA helicase DDX42
Molecular weight formula_weight	49874.9 kDa
EC 编号 ec_number	3.6.4.13
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	3802

MGHHHHHHPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMHQIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDGPIAVIVCPTRELCQQIHAECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGRLIDHVKKKATNLQRVSYLVFDEADRMFDMGFEYQVRSIASHVRPDRQTLLFSATFRKKIEKLARDILIDPIRVVQGDIGEANEDVTQIVEILHSGPSKWNWLTRRLVEFTSSGSVLLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARGLDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDLVRNLEGANQHVSKELLDLAMQNAWFRKSRFKGG

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	353

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8dpeA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	8dpeA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	42.917 Å
Unit-cell length b length_b	73.268 Å
Unit-cell length c length_c	134.041 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.531 Å
Low-resolution limit resolution_low	38.147 Å
R factor r_factor	0.2142
R_work r_work	0.2121
R_free r_free	0.2552

fit	/app/data/saxs_computation/dp/8dpe/8dpe.fit
pddf	/app/data/pr_computation/dp/8dpe/8dpe.pr.out
profile	/app/data/saxs_computation/dp/8dpe/8dpe.dat

Crystal structure of ATP-dependent RNA helicase DDX42

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

ATP-dependent RNA helicase DDX42

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