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- PDB-8tbx: Crystal structure of human DDX1 helicase in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 8tbx
TitleCrystal structure of human DDX1 helicase in complex with ADP
ComponentsATP-dependent RNA helicase DDX1
KeywordsRNA BINDING PROTEIN / DDX1 / helicase / SGC / RNA helicase
Function / homology
Function and homology information


cleavage body / tRNA-splicing ligase complex / DNA/RNA helicase activity / tRNA splicing, via endonucleolytic cleavage and ligation / protein localization to cytoplasmic stress granule / positive regulation of myeloid dendritic cell cytokine production / nuclease activity / poly(A) binding / tRNA processing in the nucleus / regulation of translational initiation ...cleavage body / tRNA-splicing ligase complex / DNA/RNA helicase activity / tRNA splicing, via endonucleolytic cleavage and ligation / protein localization to cytoplasmic stress granule / positive regulation of myeloid dendritic cell cytokine production / nuclease activity / poly(A) binding / tRNA processing in the nucleus / regulation of translational initiation / exonuclease activity / spliceosomal complex assembly / response to exogenous dsRNA / transcription coregulator activity / cytoplasmic stress granule / double-strand break repair / double-stranded RNA binding / defense response to virus / RNA helicase activity / positive regulation of canonical NF-kappaB signal transduction / RNA helicase / ribonucleoprotein complex / innate immune response / chromatin binding / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase ...RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Concanavalin A-like lectin/glucanase domain superfamily / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent RNA helicase DDX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsZeng, H. / Dong, A. / Li, Y. / Yen, H. / Hejazi, Z. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)U54 AG065187 United States
CitationJournal: To be published
Title: Crystal structure of human DDX1 helicase in complex with ADP
Authors: Zeng, H. / Dong, A. / Li, Y. / Yen, H. / Hejazi, Z. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
History
DepositionJun 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Author supporting evidence / Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9094
Polymers52,3921
Non-polymers5173
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.708, 71.517, 138.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP-dependent RNA helicase DDX1 / DEAD box protein 1 / DEAD box protein retinoblastoma / DBP-RB


Mass: 52391.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92499, RNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.04M Potassium phosphate monobasic,16%w/v PEG 8K,20% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14191 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.061 / Rrim(I) all: 0.163 / Χ2: 0.807 / Net I/σ(I): 5 / Num. measured all: 100389
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.7-2.756.90.9676910.7530.9270.3921.0460.682100
2.75-2.87.20.8837150.7740.9340.3490.9510.666100
2.8-2.857.20.8416730.7870.9380.3320.9060.687100
2.85-2.917.40.6876920.880.9670.2680.7380.693100
2.91-2.977.30.6187080.8840.9690.2420.6640.71199.9
2.97-3.047.40.5016810.9190.9790.1950.5390.744100
3.04-3.127.30.4327040.9380.9840.170.4650.716100
3.12-3.27.20.3657000.960.990.1440.3930.696100
3.2-3.37.10.2966890.9680.9920.1170.3190.75799.9
3.3-3.46.90.2517140.9730.9930.1010.2710.74999.9
3.4-3.526.50.2026960.9810.9950.0840.2190.7999.9
3.52-3.665.90.1746860.9820.9960.0760.1910.90799
3.66-3.837.40.1477060.9910.9980.0580.1590.76699.7
3.83-4.037.50.1187060.9950.9990.0460.1270.824100
4.03-4.297.50.17210.9960.9990.0390.1080.779100
4.29-4.627.30.0777170.9960.9990.0310.0830.7399.7
4.62-5.087.30.0727260.9970.9990.0290.0780.709100
5.08-5.817.10.0757200.9960.9990.030.0810.703100
5.81-7.326.10.0717420.9970.9990.030.0780.75999.3
7.32-506.80.0948040.9870.9970.040.1032.014100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→49.8 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.877 / SU B: 14.991 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28647 728 5.1 %RANDOM
Rwork0.20257 ---
obs0.20678 13419 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.552 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å2-0 Å2
2---2.52 Å20 Å2
3---0.87 Å2
Refinement stepCycle: 1 / Resolution: 2.71→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 29 12 3476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133527
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173205
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.6344796
X-RAY DIFFRACTIONr_angle_other_deg1.2151.5737419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4145455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35423.478161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88915567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9791516
X-RAY DIFFRACTIONr_chiral_restr0.0530.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023969
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02678
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1575.2851829
X-RAY DIFFRACTIONr_mcbond_other4.1585.2851828
X-RAY DIFFRACTIONr_mcangle_it6.3617.9172281
X-RAY DIFFRACTIONr_mcangle_other6.367.9172282
X-RAY DIFFRACTIONr_scbond_it4.0815.3751698
X-RAY DIFFRACTIONr_scbond_other4.0815.3751698
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3047.9642516
X-RAY DIFFRACTIONr_long_range_B_refined9.41562.0083776
X-RAY DIFFRACTIONr_long_range_B_other9.41462.0053777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.715→2.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 53 -
Rwork0.25 925 -
obs--94.77 %

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