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5e7m

Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 bound to AMPPNP

Method: X-RAY DIFFRACTION Dmax: 78.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP-dependent RNA helicase DDX3X

Homo sapiens

UniProt O00571

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 133–584 Fragment：DEAD-box domains ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG-3000, sodium citrate Resolution 2.30 Å R-free 0.284

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 5E7M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2I4I Crystal Structure of human DEAD-box RNA helicase DDX3X Deposited 2006-08-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 167–581（415 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；1.75M Na formate, 0.1M Tris pH 7.5, 20mM ATPgS and MgCl2, VAPOR DIFFUSION, temperature 277K
Resolution 2.20 Å R-free 0.218
2JGN DDX3 helicase domain Deposited 2007-02-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 408–579（172 aa） Fragment：HELICASE DOMAIN, RESIDUES 408-579
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions RESERVOIR: 2M (NH4)2SO4, 0.1M IMIDAZOLE PH 6.4 PLUS 5MM SPERMINE TETRA-HCL PROTEIN: 10MM HEPES, 500MM (NH4)2SO4, PH 8.0.
Resolution 1.91 Å R-free 0.255
2JGN DDX3 helicase domain Deposited 2007-02-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 408–579（172 aa） Fragment：HELICASE DOMAIN, RESIDUES 408-579
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions RESERVOIR: 2M (NH4)2SO4, 0.1M IMIDAZOLE PH 6.4 PLUS 5MM SPERMINE TETRA-HCL PROTEIN: 10MM HEPES, 500MM (NH4)2SO4, PH 8.0.
Resolution 1.91 Å R-free 0.255
2JGN DDX3 helicase domain Deposited 2007-02-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 408–579（172 aa） Fragment：HELICASE DOMAIN, RESIDUES 408-579
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions RESERVOIR: 2M (NH4)2SO4, 0.1M IMIDAZOLE PH 6.4 PLUS 5MM SPERMINE TETRA-HCL PROTEIN: 10MM HEPES, 500MM (NH4)2SO4, PH 8.0.
Resolution 1.91 Å R-free 0.255
3JRV Structure of poxvirus K7 protein in complex with RNA helicase DDX3 Deposited 2009-09-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 71–90（20 aa） Fragment：DDX3, UNP residues 71-90
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；100mM sodium citrate, 15.0% (w/v) PEG 3350, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.60 Å R-free 0.190
3JRV Structure of poxvirus K7 protein in complex with RNA helicase DDX3 Deposited 2009-09-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 71–90（20 aa） Fragment：DDX3, UNP residues 71-90
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；100mM sodium citrate, 15.0% (w/v) PEG 3350, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.60 Å R-free 0.190
3JRV Structure of poxvirus K7 protein in complex with RNA helicase DDX3 Deposited 2009-09-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 71–90（20 aa） Fragment：DDX3, UNP residues 71-90
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；100mM sodium citrate, 15.0% (w/v) PEG 3350, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.60 Å R-free 0.190
4O2C An Nt-acetylated peptide complexed with HLA-B*3901 Deposited 2013-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–10（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M ammonium acetate, 0.1M Bis-Tris (pH 6.5), 17% (w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.202
4O2E A peptide complexed with HLA-B*3901 Deposited 2013-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–10（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M ammonium acetate, 0.1M Bis-Tris (pH 6.5), 20% (w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.98 Å R-free 0.208
4O2E A peptide complexed with HLA-B*3901 Deposited 2013-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 2–10（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M ammonium acetate, 0.1M Bis-Tris (pH 6.5), 20% (w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.98 Å R-free 0.208
4O2F A peptide complexed with HLA-B*3901 Deposited 2013-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 3–10（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2M sodium formate, 20% (w/v) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.213
4O2F A peptide complexed with HLA-B*3901 Deposited 2013-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 3–10（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2M sodium formate, 20% (w/v) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.213
4PX9 DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop Deposited 2014-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 135–407（273 aa） Fragment：UNP residues 135-407
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；50 mM Hepes 7.6; 7% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.31 Å R-free 0.285
4PX9 DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop Deposited 2014-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 135–407（273 aa） Fragment：UNP residues 135-407
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；50 mM Hepes 7.6; 7% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.31 Å R-free 0.285
4PX9 DEAD-box RNA helicase DDX3X Domain 1 with N-terminal ATP-binding Loop Deposited 2014-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 135–407（273 aa） Fragment：UNP residues 135-407
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；50 mM Hepes 7.6; 7% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.31 Å R-free 0.285
4PXA DEAD-box RNA helicase DDX3X Cancer-associated mutant D354V Deposited 2014-03-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 135–582（448 aa） Fragment：D1-D2, UNP residues 135-582
Mutation：D354V ADP ADENOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.66 M NaH2PO4 0.24 M K2HPO4, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 3.20 Å R-free 0.271
5E7I Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 Deposited 2015-10-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 133–584（452 aa） Fragment：DEAD-box domains
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3350, sodium citrate
Resolution 2.22 Å R-free 0.259
5E7I Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 Deposited 2015-10-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–584（452 aa） Fragment：DEAD-box domains
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3350, sodium citrate
Resolution 2.22 Å R-free 0.259
5E7I Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 Deposited 2015-10-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 133–584（452 aa） Fragment：DEAD-box domains
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3350, sodium citrate
Resolution 2.22 Å R-free 0.259
5E7J Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 bound to AMP Deposited 2015-10-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–584（452 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3000, sodium citrate
Resolution 2.23 Å R-free 0.264
6CZ5 Crystal structure of small molecule AMP-acrylamide covalently bound to DDX3 S228C Deposited 2018-04-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 132–607（476 aa） Fragment：UNP residues 132-607
Mutation：S228C FPJ 5'-O-[(R)-hydroxy(propanoylamino)phosphoryl]adenosine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；100 mM sodium citrate, 8% PEG3000
Resolution 3.00 Å R-free 0.267
6O5F Crystal structure of DEAD-box RNA helicase DDX3X at pre-unwound state Deposited 2019-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 132–607（476 aa）
Chain B 132–607（476 aa）
Not recorded CL CHLORIDE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；25% (v/v) PEG 3350, 0.2 M magnesium chloride, 0.1 M Tris pH 8.5
Resolution 2.50 Å R-free 0.246
7LIU DDX3X bound to ATP analog and remodeled RNA:DNA hybrid Deposited 2021-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 135–582（448 aa）
Chain B 135–582（448 aa）
Not recorded MG MAGNESIUM ION × 2 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M HEPEs pH 7.5, 16% PEG 3350, 0.1 M Li3Citrate, 0.1 M Na3Citrate, 2% benzamidine-HCl, 5 mM ADP-BeF3
Resolution 3.00 Å R-free 0.241
7YMF Crystal Structure of DDX3X449_450ET>DP Deposited 2022-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 133–414（282 aa）
Chain B 415–584（170 aa）
Mutation：E449D, T450P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES pH 6.5, 1.5 M Sodium Formate , 50 mM Magnesium chloride
Resolution 2.30 Å R-free 0.244
8SSW Crystal structure of DEAD-box RNA helicase DDX3X in complex with ADP at pre-unwound state Deposited 2023-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 132–607（476 aa）
Chain B 132–607（476 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG3350, Magnesium Chloride, etc.
Resolution 2.40 Å R-free 0.248
9E2C Crystal structure of DEAD-box RNA helicase DDX3X R326H mutant Deposited 2024-10-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 115–591（477 aa）
Mutation：R326H GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；0.1 M Bis-Tris pH 5.5, 25% PEG3350, 0.2 M Lithium sulfate, 0.01 M Strontium(II) chloride
Resolution 2.30 Å R-free 0.244

16 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DDX3X_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–452； UniProt 133–584

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 5e7m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5e7m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5e7m
Deposition date deposition_date2015-10-12
Structure title titleCrystal structure of the active catalytic core of the human DEAD-box protein DDX3 bound to AMPPNP
Keywords keywordsDEAD-box protein, RNA helicase, RecA fold, HYDROLASE; HYDROLASE
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_guinier24.28 Å
Radius of gyration Rg (electron density) rg_electron23.28 Å
Forward intensity I(0) i040499500.00
Molecular weight molecular_weight48257.0 kDa
Excluded volume excluded_volume60141 ų
Envelope volume envelope_volume72751 ų
Hydration-shell volume shell_volume26172 ų
Envelope diameter envelope_diameter78.6 Å
Shell Rg shell_rg30.51 Å
Envelope Rg envelope_rg23.43 Å
Shape Rg shape_rg23.32 Å
Total Rg total_rg24.03 Å
Total atoms total_atoms3385
Residues n_residues424
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 dmax78.2 Å
Rg (real space) rg_real24.25 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real4.0500e+07
I(0) uncertainty (real space) i0_real_error5.7560e+05
Rg (reciprocal space) rg_reciprocal24.26 Å
I(0) (reciprocal space) i0_reciprocal40500000.0000
Solution quality estimate total_estimate0.8941
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6 Å
Skewness Skewness skewness0.345
Kurtosis Kurtosis kurtosis-0.339
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12770000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.982
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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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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5e7mA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5e7mA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)