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- PDB-2hxy: Crystal structure of human apo-eIF4AIII -

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Basic information

Entry
Database: PDB / ID: 2hxy
TitleCrystal structure of human apo-eIF4AIII
ComponentsProbable ATP-dependent RNA helicase DDX48
KeywordsHYDROLASE / helicase / ATPase
Function / homology
Function and homology information


negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / negative regulation of excitatory postsynaptic potential / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / U2-type catalytic step 1 spliceosome ...negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / negative regulation of excitatory postsynaptic potential / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / U2-type catalytic step 1 spliceosome / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / RNA stem-loop binding / mRNA 3'-end processing / embryonic cranial skeleton morphogenesis / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exploration behavior / associative learning / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribonucleoprotein complex binding / mRNA export from nucleus / cellular response to brain-derived neurotrophic factor stimulus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of translation / response to organic cyclic compound / ISG15 antiviral mechanism / mRNA splicing, via spliceosome / rRNA processing / Regulation of expression of SLITs and ROBOs / postsynapse / negative regulation of translation / RNA helicase activity / RNA helicase / nuclear speck / mRNA binding / dendrite / neuronal cell body / glutamatergic synapse / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / 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
Eukaryotic initiation factor 4A-III
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsJohansen, J.S. / Andersen, G.R.
CitationJournal: Science / Year: 2006
Title: Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA.
Authors: Andersen, C.B. / Ballut, L. / Johansen, J.S. / Chamieh, H. / Nielsen, K.H. / Oliveira, C.L. / Pedersen, J.S. / Seraphin, B. / Le Hir, H. / Andersen, G.R.
History
DepositionAug 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX48
B: Probable ATP-dependent RNA helicase DDX48
C: Probable ATP-dependent RNA helicase DDX48
D: Probable ATP-dependent RNA helicase DDX48


Theoretical massNumber of molelcules
Total (without water)179,2744
Polymers179,2744
Non-polymers00
Water0
1
A: Probable ATP-dependent RNA helicase DDX48


Theoretical massNumber of molelcules
Total (without water)44,8191
Polymers44,8191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ATP-dependent RNA helicase DDX48


Theoretical massNumber of molelcules
Total (without water)44,8191
Polymers44,8191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable ATP-dependent RNA helicase DDX48


Theoretical massNumber of molelcules
Total (without water)44,8191
Polymers44,8191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Probable ATP-dependent RNA helicase DDX48


Theoretical massNumber of molelcules
Total (without water)44,8191
Polymers44,8191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.220, 238.050, 79.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Probable ATP-dependent RNA helicase DDX48 / DEAD box protein 48 / Eukaryotic initiation factor 4A-like NUK-34 / Nuclear matrix protein 265 / ...DEAD box protein 48 / Eukaryotic initiation factor 4A-like NUK-34 / Nuclear matrix protein 265 / hNMP 265 / Eukaryotic translation initiation factor 4A isoform 3


Mass: 44818.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX48, EIF4A3, KIAA0111 / Production host: Escherichia coli (E. coli)
References: UniProt: P38919, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: Ammonium Citrate, pH 7.5, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 43848 / Num. obs: 43678 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.88 % / Rsym value: 0.153 / Net I/σ(I): 11.4
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.86 / Rsym value: 0.668 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.308 1335 Thin resolution shells
Rwork0.275 --
all0.276 43804 -
obs0.276 43678 -
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12080 0 0 0 12080
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_bond_d0.0109

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