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- PDB-5e7i: Crystal structure of the active catalytic core of the human DEAD-... -

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Basic information

Entry
Database: PDB / ID: 5e7i
TitleCrystal structure of the active catalytic core of the human DEAD-box protein DDX3
ComponentsATP-dependent RNA helicase DDX3X
KeywordsHYDROLASE / DEAD-box protein / RNA helicase / RecA fold
Function / homology
Function and homology information


positive regulation of protein acetylation / CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of chemokine (C-C motif) ligand 5 production / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / RNA secondary structure unwinding ...positive regulation of protein acetylation / CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of chemokine (C-C motif) ligand 5 production / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / RNA secondary structure unwinding / gamete generation / NLRP3 inflammasome complex / positive regulation of protein K63-linked ubiquitination / cellular response to arsenic-containing substance / poly(A) binding / P granule / RNA stem-loop binding / cellular response to osmotic stress / gamma-tubulin binding / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of NLRP3 inflammasome complex assembly / cell leading edge / lipid homeostasis / positive regulation of interferon-alpha production / ribosomal small subunit binding / positive regulation of translational initiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / transcription factor binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of viral genome replication / negative regulation of protein-containing complex assembly / negative regulation of intrinsic apoptotic signaling pathway / signaling adaptor activity / stress granule assembly / translation initiation factor binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / translational initiation / positive regulation of protein autophosphorylation / DNA helicase activity / positive regulation of interferon-beta production / protein serine/threonine kinase activator activity / ribonucleoside triphosphate phosphatase activity / intrinsic apoptotic signaling pathway / cytosolic ribosome assembly / positive regulation of translation / chromosome segregation / response to virus / mRNA 5'-UTR binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein serine/threonine kinase activity / negative regulation of cell growth / Wnt signaling pathway / cellular response to virus / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of cell growth / secretory granule lumen / ficolin-1-rich granule lumen / negative regulation of translation / RNA helicase activity / cell differentiation / RNA helicase / intracellular signal transduction / cadherin binding / positive regulation of apoptotic process / mRNA binding / innate immune response / GTPase activity / centrosome / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. ...DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.223 Å
AuthorsFloor, S.N. / Condon, K.J. / Doudna, J.A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3.
Authors: Floor, S.N. / Condon, K.J. / Sharma, D. / Jankowsky, E. / Doudna, J.A.
History
DepositionOct 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ATP-dependent RNA helicase DDX3X
A: ATP-dependent RNA helicase DDX3X
C: ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)153,2763
Polymers153,2763
Non-polymers00
Water0
1
B: ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)51,0921
Polymers51,0921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)51,0921
Polymers51,0921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)51,0921
Polymers51,0921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.710, 105.380, 94.610
Angle α, β, γ (deg.)90.000, 114.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent RNA helicase DDX3X / DEAD box protein 3 / X-chromosomal / DEAD box / X isoform / Helicase-like protein 2 / HLP2


Mass: 51092.000 Da / Num. of mol.: 3 / Fragment: DEAD-box domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX3X, DBX, DDX3 / Plasmid: pHMGWA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: O00571, RNA helicase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 3350, sodium citrate / PH range: 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.22→86.06 Å / Num. obs: 79724 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 32.82 Å2 / Rmerge F obs: 0.991 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.187 / Χ2: 0.953 / Net I/σ(I): 8.14 / Num. measured all: 311833
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.22-2.280.3691.3610.9212340601946741.67377.7
2.28-2.340.4151.1231.2419148583955691.33295.4
2.34-2.410.4861.0411.5822900569356791.20199.8
2.41-2.490.5730.8961.9222423552755151.03199.8
2.49-2.570.6610.7372.2921758538253690.84999.8
2.57-2.660.7310.6382.6121057519651810.73599.7
2.66-2.760.7790.5113.2620187499149810.58999.8
2.76-2.870.8660.3954.1519532481448060.45699.8
2.87-30.9190.3015.2818733462546120.34799.7
3-3.140.9460.2396.4717967441544090.27599.9
3.14-3.310.970.1698.7617038419841890.19499.8
3.31-3.520.9820.12611.3216158400739970.14699.8
3.52-3.760.9890.09713.9415046375437440.11299.7
3.76-4.060.9930.07716.9113974350734940.08999.6
4.06-4.450.9960.05721.2812766319931890.06599.7
4.45-4.970.9970.0523.4711554291129050.05899.8
4.97-5.740.9960.05919.9210182258125710.06899.6
5.74-7.030.9950.06119.228575220321920.0799.5
7.03-9.940.9980.03827.846799170316930.04499.4
9.940.9980.02935.2136969729550.03498.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.223→86.06 Å / FOM work R set: 0.7813 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 3985 5 %
Rwork0.2257 75698 -
obs0.2274 79683 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.43 Å2 / Biso mean: 46.72 Å2 / Biso min: 10.25 Å2
Refinement stepCycle: final / Resolution: 2.223→86.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10060 0 0 0 10060
Num. residues----1272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410247
X-RAY DIFFRACTIONf_angle_d0.81613838
X-RAY DIFFRACTIONf_chiral_restr0.0311542
X-RAY DIFFRACTIONf_plane_restr0.0041809
X-RAY DIFFRACTIONf_dihedral_angle_d14.5073911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2233-2.25050.437980.42751843194166
2.2505-2.2790.44331240.43532337246188
2.279-2.30890.34861370.32182607274493
2.3089-2.34060.36331400.30942642278297
2.3406-2.3740.34571450.303127592904100
2.374-2.40950.35731450.307927522897100
2.4095-2.44710.30931430.289227232866100
2.4471-2.48720.30611450.285427532898100
2.4872-2.53010.34651440.284127482892100
2.5301-2.57610.30091460.28527742920100
2.5761-2.62570.33041450.277727362881100
2.6257-2.67930.30031440.277227402884100
2.6793-2.73750.27781450.269927572902100
2.7375-2.80120.29381450.268927572902100
2.8012-2.87130.32931440.263827422886100
2.8713-2.94890.26631450.25627432888100
2.9489-3.03570.3371460.258427732919100
3.0357-3.13370.27251440.25327372881100
3.1337-3.24570.27781460.243527782924100
3.2457-3.37560.26271470.233127872934100
3.3756-3.52930.26271420.220927152857100
3.5293-3.71540.26441470.203127852932100
3.7154-3.94810.21361460.188527692915100
3.9481-4.2530.20441460.182327722918100
4.253-4.68090.17581450.152827542899100
4.6809-5.35820.20631460.161527842930100
5.3582-6.75040.22581480.197428072955100
6.7504-86.12580.19851470.159328242971100

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