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- PDB-2g9n: Structure of the DEAD domain of Human eukaryotic initiation facto... -

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Basic information

Entry
Database: PDB / ID: 2g9n
TitleStructure of the DEAD domain of Human eukaryotic initiation factor 4A, eIF4A
ComponentsEukaryotic initiation factor 4A-I
KeywordsHYDROLASE / DEAD-box / Helicase / DDX2A / RNA / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / RNA cap binding / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / cytoplasmic translational initiation / translation factor activity, RNA binding / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Ribosomal scanning and start codon recognition / Translation initiation complex formation ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / RNA cap binding / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / cytoplasmic translational initiation / translation factor activity, RNA binding / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Ribosomal scanning and start codon recognition / Translation initiation complex formation / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / translational initiation / translation initiation factor activity / helicase activity / ISG15 antiviral mechanism / double-stranded RNA binding / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / 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. ...ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / 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-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHogbom, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. ...Hogbom, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hallberg, B.M. / Hammarstrom, M. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Uppenberg, J. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Comparative Structural Analysis of Human DEAD-Box RNA Helicases.
Authors: Schutz, P. / Karlberg, T. / van den Berg, S. / Collins, R. / Lehtio, L. / Hogbom, M. / Holmberg-Schiavone, L. / Tempel, W. / Park, H.W. / Hammarstrom, M. / Moche, M. / Thorsell, A.G. / Schuler, H.
History
DepositionMar 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic initiation factor 4A-I
B: Eukaryotic initiation factor 4A-I


Theoretical massNumber of molelcules
Total (without water)50,1752
Polymers50,1752
Non-polymers00
Water4,071226
1
A: Eukaryotic initiation factor 4A-I


Theoretical massNumber of molelcules
Total (without water)25,0871
Polymers25,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic initiation factor 4A-I


Theoretical massNumber of molelcules
Total (without water)25,0871
Polymers25,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.799, 78.252, 59.088
Angle α, β, γ (deg.)90.00, 103.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEILEILEAA30 - 13513 - 118
21ILEILEILEILEBB30 - 13513 - 118
32ALAALALEULEUAA151 - 235134 - 218
42ALAALALEULEUBB151 - 235134 - 218

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Components

#1: Protein Eukaryotic initiation factor 4A-I / ATP-dependent RNA helicase eIF4A-1 / eIF4A-I / eIF-4A-I


Mass: 25087.316 Da / Num. of mol.: 2 / Fragment: DEAD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A1, DDX2A, EIF4A / Plasmid: pNIC-28-Bsa1 / Production host: Escherichia coli (E. coli)
References: UniProt: P60842, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 200 mM Ammonium Nitrate, 500 mM NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2006
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 19100 / Num. obs: 19100 / % possible obs: 99.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.071 / Net I/σ(I): 7.4
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.46 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 2912 / Rsym value: 0.241 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1QDE

1qde


Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.882 / SU B: 12.622 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 1026 5.1 %RANDOM
Rwork0.1761 ---
all0.18026 19100 --
obs0.18026 19100 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.56 Å2
2--1.49 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 0 226 3657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223482
X-RAY DIFFRACTIONr_angle_refined_deg1.7322.0254558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.035379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06324.865148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30115536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6231520
X-RAY DIFFRACTIONr_chiral_restr0.1270.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022308
X-RAY DIFFRACTIONr_nbd_refined0.2350.21689
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22339
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2198
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3410.212
X-RAY DIFFRACTIONr_mcbond_it0.9121.52224
X-RAY DIFFRACTIONr_mcangle_it1.38423318
X-RAY DIFFRACTIONr_scbond_it2.43331415
X-RAY DIFFRACTIONr_scangle_it3.8124.51240
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1514 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.560.5
medium thermal1.062
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 61 -
Rwork0.187 1422 -
obs--100 %

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