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- PDB-3llm: Crystal Structure Analysis of a RNA Helicase -

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Basic information

Entry
Database: PDB / ID: 3llm
TitleCrystal Structure Analysis of a RNA Helicase
ComponentsATP-dependent RNA helicase A
KeywordsHYDROLASE / alpha-beta-alpha / Structural Genomics / Structural Genomics Consortium / SGC / Activator / ATP-binding / DNA-binding / Helicase / Methylation / Nucleotide-binding / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


single-stranded 3'-5' DNA helicase activity / positive regulation of viral translation / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulation of cytoplasmic translation / regulatory region RNA binding / : / positive regulation of RNA export from nucleus / DNA-templated viral transcription / positive regulation of viral transcription ...single-stranded 3'-5' DNA helicase activity / positive regulation of viral translation / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulation of cytoplasmic translation / regulatory region RNA binding / : / positive regulation of RNA export from nucleus / DNA-templated viral transcription / positive regulation of viral transcription / RISC complex binding / triplex DNA binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / G-quadruplex DNA unwinding / nucleoside triphosphate diphosphatase activity / nuclear stress granule / 3'-5' RNA helicase activity / perichromatin fibrils / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RNA secondary structure unwinding / positive regulation of interleukin-18 production / alternative mRNA splicing, via spliceosome / RISC-loading complex / regulation of mRNA processing / miRNA-mediated post-transcriptional gene silencing / RISC complex assembly / regulation of defense response to virus by host / positive regulation of cytoplasmic translation / importin-alpha family protein binding / siRNA binding / RIP-mediated NFkB activation via ZBP1 / positive regulation of response to cytokine stimulus / RNA stem-loop binding / positive regulation of innate immune response / RISC complex / sequence-specific mRNA binding / RNA polymerase binding / 3'-5' DNA helicase activity / DNA duplex unwinding / RNA polymerase II complex binding / cellular response to exogenous dsRNA / DNA replication origin binding / pyroptotic inflammatory response / positive regulation of interferon-alpha production / mRNA transport / positive regulation of DNA repair / DNA helicase activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / mRNA Splicing - Major Pathway / positive regulation of DNA replication / promoter-specific chromatin binding / DNA-templated transcription termination / transcription coregulator activity / PKR-mediated signaling / cytoplasmic ribonucleoprotein granule / chromatin DNA binding / osteoblast differentiation / positive regulation of inflammatory response / positive regulation of interleukin-6 production / rhythmic process / positive regulation of fibroblast proliferation / ribosome binding / actin cytoskeleton / positive regulation of tumor necrosis factor production / single-stranded DNA binding / double-stranded RNA binding / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / double-stranded DNA binding / protein-containing complex assembly / RNA polymerase II-specific DNA-binding transcription factor binding / DNA replication / RNA helicase activity / single-stranded RNA binding / transcription coactivator activity / nuclear body / RNA helicase / inflammatory response / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mRNA binding / innate immune response / centrosome / nucleolus / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / Double-stranded RNA binding motif / Double-stranded RNA binding motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / 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
ADENOSINE-5'-DIPHOSPHATE / CACODYLATE ION / : / ATP-dependent RNA helicase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSchutz, P. / Karlberg, T. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. ...Schutz, P. / Karlberg, T. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Kraulis, P. / Kotenyova, T. / Kotzsch, A. / Markova, N. / Moche, M. / Nielsen, T.K. / Nordlund, P. / Nyman, T. / Persson, C. / Roos, A.K. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H.M. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of human RNA helicase A (DHX9): structural basis for unselective nucleotide base binding in a DEAD-box variant protein.
Authors: Schutz, P. / Wahlberg, E. / Karlberg, T. / Hammarstrom, M. / Collins, R. / Flores, A. / Schuler, H.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,7258
Polymers53,5322
Non-polymers1,1936
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-37 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.700, 113.700, 141.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A329 - 563
2115B329 - 563

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATP-dependent RNA helicase A / Nuclear DNA helicase II / NDH II / DEAH box protein 9


Mass: 26765.787 Da / Num. of mol.: 2 / Fragment: Nucleotide binding domain (UNP residues 329-563)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX9, DHX9, LKP, NDH2 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 pRARE
References: UniProt: Q08211, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 5 types, 33 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 4.94 Å3/Da / Density % sol: 75.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08 M Sodium cacodylate, 0.16 M Calcium acetate hydrate, 14.4 % PEG 8000, 20 % glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98000, 0.98020, 0.96860
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.98021
30.96861
ReflectionResolution: 2.8→98.51 Å / Num. all: 26628 / Num. obs: 26628 / % possible obs: 100 % / Redundancy: 10.8 % / Rsym value: 0.099 / Net I/σ(I): 14.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 0.7 / Num. measured all: 42589 / Num. unique all: 3834 / Rsym value: 1.041 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
GDAdata collection
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→98.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.989 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1343 5 %RANDOM
Rwork0.211 ---
obs0.212 26598 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 165.68 Å2 / Biso mean: 65.358 Å2 / Biso min: 42.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å20 Å2
2--0.82 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.8→98.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 67 27 3773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223826
X-RAY DIFFRACTIONr_bond_other_d0.0010.022556
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9835216
X-RAY DIFFRACTIONr_angle_other_deg0.88436251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6115468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26324.379169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38715635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7331526
X-RAY DIFFRACTIONr_chiral_restr0.0730.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214180
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
X-RAY DIFFRACTIONr_mcbond_it0.6591.52356
X-RAY DIFFRACTIONr_mcbond_other0.1131.5930
X-RAY DIFFRACTIONr_mcangle_it1.32623855
X-RAY DIFFRACTIONr_scbond_it2.03331470
X-RAY DIFFRACTIONr_scangle_it3.4284.51361
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1385MEDIUM POSITIONAL0.430.5
1672LOOSE POSITIONAL0.715
1385MEDIUM THERMAL0.632
1672LOOSE THERMAL0.710
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 82 -
Rwork0.395 1844 -
all-1926 -
obs--100 %

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