ATP-dependent RNA helicase DDX3X
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 167–581 | 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 |
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 2I4I | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 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 construct 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 construct 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 construct 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 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 |
| 5E7M Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 bound to AMPPNP 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)
Fragment:DEAD-box domains
|
Not recorded | 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 |
| 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 3–417; UniProt 167–581 |