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- PDB-4xw3: Crystal structure of the SPRY domain of the human DEAD-box protei... -

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Basic information

Entry
Database: PDB / ID: 4xw3
TitleCrystal structure of the SPRY domain of the human DEAD-box protein DDX1
ComponentsATP-dependent RNA helicase DDX1
KeywordsHYDROLASE / beta-sandwich / insertion domain / DEAD-box protein / SPRY domain
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 ...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 / tRNA processing / DNA duplex unwinding / spliceosomal complex assembly / response to exogenous dsRNA / transcription coregulator activity / cytoplasmic stress granule / double-stranded RNA binding / double-strand break repair / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / RNA helicase activity / RNA helicase / ribonucleoprotein complex / innate immune response / chromatin binding / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
SPRY domain / 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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / DEAD/DEAH box helicase ...SPRY domain / 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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Helicase superfamily 1/2, ATP-binding domain / Jelly Rolls / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DDX1 / ATP-dependent RNA helicase DDX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKellner, J.N. / Meinhart, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationME 3135/1-2 Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein.
Authors: Kellner, J.N. / Meinhart, A.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX1
B: ATP-dependent RNA helicase DDX1


Theoretical massNumber of molelcules
Total (without water)49,2902
Polymers49,2902
Non-polymers00
Water2,558142
1
A: ATP-dependent RNA helicase DDX1


Theoretical massNumber of molelcules
Total (without water)24,6451
Polymers24,6451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase DDX1


Theoretical massNumber of molelcules
Total (without water)24,6451
Polymers24,6451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.060, 76.140, 122.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein ATP-dependent RNA helicase DDX1 / DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 / isoform CRA_d / DEAD box polypeptide 1 / cDNA / FLJ94573 ...DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 / isoform CRA_d / DEAD box polypeptide 1 / cDNA / FLJ94573 / Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 (DDX1) / mRNA


Mass: 24644.887 Da / Num. of mol.: 2 / Fragment: unp residues 72-283
Source method: isolated from a genetically manipulated source
Details: cDNA / Source: (gene. exp.) Homo sapiens (human) / Gene: DDX1, hCG_15914 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus- RIL / References: UniProt: A3RJH1, UniProt: Q92499*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.45 % / Description: spheroid crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 35 % (v/v) PEG 600, 0.1 M tri-Sodium-citrate pH 5.5 - crystals appeared after 3 days and grew as single crystals
PH range: 5 - 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.06998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06998 Å / Relative weight: 1
ReflectionResolution: 2→47.78 Å / Num. obs: 28891 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 12.71 % / Biso Wilson estimate: 32.683 Å2 / Rmerge F obs: 0.074 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.079 / Χ2: 0.996 / Net I/σ(I): 23.63 / Num. measured all: 367329
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.112.690.3030.5636.5248403391038150.58697.6
2.1-2.20.210.418.942646324531700.42697.7
2.2-2.40.1510.28511.7665065500549070.29698
2.4-2.60.1230.19514.9643466356335120.20498.6
2.6-2.70.0830.13819.3918075142414040.14398.6
2.7-2.80.0650.11622.316593124412300.12198.9
2.8-30.0490.08627.0226100198319560.0998.6
3-40.0290.04837.0361154506250330.0599.4
4-60.0150.02957.0432537266326550.0399.7
6-100.0140.02559.21103049299260.02799.7
100.0110.02267.6129862852830.02399.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.76 Å
Translation2.5 Å47.76 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSVERSION December 29, 2011data reduction
PHASER1.3.3phasing
PDB_EXTRACT3.15data extraction
XSCALEVERSION December 29, 2011data scaling
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3toj

3toj


Resolution: 2→47.78 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.107 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 1445 5 %RANDOM
Rwork0.1997 27446 --
obs0.2015 28891 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.28 Å2 / Biso mean: 28.267 Å2 / Biso min: 12.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----1.5 Å2
Refinement stepCycle: final / Resolution: 2→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 0 0 142 3144
Biso mean---33.98 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213082
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9334134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90224.73148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98915530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.326158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022384
X-RAY DIFFRACTIONr_nbd_refined0.1850.21179
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.219
X-RAY DIFFRACTIONr_mcbond_it0.6291.51938
X-RAY DIFFRACTIONr_mcangle_it1.06522988
X-RAY DIFFRACTIONr_scbond_it1.63931302
X-RAY DIFFRACTIONr_scangle_it2.4574.51146
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 104 -
Rwork0.212 1983 -
all-2087 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9068-0.0821-0.12672.17230.05064.06530.04140.02950.02730.0119-0.03890.05750.005-0.0094-0.0025-0.1603-0.00690.0053-0.15260.0056-0.1254-2.1144-1.766510.58
22.2751-0.1164-0.15252.307-0.11523.76420.0217-0.0404-0.0265-0.0318-0.02280.0640.045-0.04040.0011-0.16060.0033-0.0079-0.15520.0011-0.131320.19111.9971-15.7642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 275
2X-RAY DIFFRACTION2B86 - 279

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