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- PDB-8kca: Crystal structure of DDX53 helicase domain -

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Basic information

Entry
Database: PDB / ID: 8kca
TitleCrystal structure of DDX53 helicase domain
ComponentsProbable ATP-dependent RNA helicase DDX53
KeywordsRNA BINDING PROTEIN / RNA helicase
Function / homology
Function and homology information


RNA helicase activity / RNA helicase / intracellular membrane-bounded organelle / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / cytosol
Similarity search - Function
KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / K Homology domain, type 1 superfamily / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain ...KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / K Homology domain, type 1 superfamily / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / K Homology domain / K homology RNA-binding 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Probable ATP-dependent RNA helicase DDX53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsPark, S. / Yang, J.B. / Jung, H.S. / Kim, H.Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C1009404 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1F1A1060031 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural insight into crystal structure of helicase domain of DDX53.
Authors: Park, S. / Yang, J.B. / Park, Y.H. / Kim, Y.K. / Jeoung, D. / Kim, H.Y. / Jung, H.S.
History
DepositionAug 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX53
B: Probable ATP-dependent RNA helicase DDX53


Theoretical massNumber of molelcules
Total (without water)44,1062
Polymers44,1062
Non-polymers00
Water1,964109
1
A: Probable ATP-dependent RNA helicase DDX53


Theoretical massNumber of molelcules
Total (without water)22,0531
Polymers22,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ATP-dependent RNA helicase DDX53


Theoretical massNumber of molelcules
Total (without water)22,0531
Polymers22,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.866, 106.494, 41.943
Angle α, β, γ (deg.)90.000, 98.610, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Probable ATP-dependent RNA helicase DDX53 / Cancer-associated gene protein / Cancer/testis antigen 26 / CT26 / DEAD box protein 53 / DEAD box protein CAGE


Mass: 22052.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX53, CAGE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86TM3, RNA helicase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 1 M trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. obs: 24420 / % possible obs: 96.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.3
Reflection shellResolution: 1.97→2.04 Å / Rmerge(I) obs: 0.64 / Num. unique obs: 2193 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→27.32 Å / SU ML: 0.2503 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.3518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2314 1984 8.17 %
Rwork0.1852 22309 -
obs0.189 24293 95.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.91 Å2
Refinement stepCycle: LAST / Resolution: 1.97→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 0 109 2861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872834
X-RAY DIFFRACTIONf_angle_d1.12693829
X-RAY DIFFRACTIONf_chiral_restr0.0638441
X-RAY DIFFRACTIONf_plane_restr0.0107505
X-RAY DIFFRACTIONf_dihedral_angle_d5.9126383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.36031160.30361307X-RAY DIFFRACTION79.14
2.02-2.080.29921270.2731469X-RAY DIFFRACTION87.21
2.08-2.140.31881420.2471567X-RAY DIFFRACTION95.9
2.14-2.210.29741540.22951668X-RAY DIFFRACTION97.59
2.21-2.290.26191390.21341586X-RAY DIFFRACTION97.35
2.29-2.380.29771430.21361640X-RAY DIFFRACTION97.17
2.38-2.490.31411400.21341596X-RAY DIFFRACTION96.02
2.49-2.620.23981470.20111631X-RAY DIFFRACTION97.05
2.62-2.780.22681450.20621638X-RAY DIFFRACTION98.29
2.78-30.26491460.1961652X-RAY DIFFRACTION98.31
3-3.30.22511390.18411589X-RAY DIFFRACTION95.89
3.3-3.770.21671470.16931655X-RAY DIFFRACTION99.12
3.77-4.750.18521430.14611645X-RAY DIFFRACTION97.55
4.75-27.320.19371560.16161666X-RAY DIFFRACTION98.01
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)
10.941290524249-0.2203124640970.1737481914691.45159433757-0.2295002712191.68821081480.01223079519570.0861405606352-0.00284005409747-0.0301627801189-0.0339732112528-0.03459065213540.006297652873730.0134918267961-2.20596705258E-50.2099242029590.002164428849640.02301690900040.2217487652620.005480546757270.232175547824-9.99771466774-24.427223547611.2318515794
21.266066649620.2890224523720.1076336663681.250003827420.01833434856670.827384085567-0.062823028549-0.06949071169380.06222657575-0.0323922572198-0.0252193595228-0.0625711529667-0.08446273290920.0774677907876-0.0001671116821050.2825993800050.01537180585680.005455247418440.2105696948820.02330790460030.2673606605476.912111716422.1444003376413.1514392889
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 440 - 612 / Label seq-ID: 1 - 173

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 440 through 612)AA
22(chain 'B' and resid 440 through 612)BB

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