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- PDB-3bor: Crystal structure of the DEADc domain of human translation initia... -

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Basic information

Entry
Database: PDB / ID: 3bor
TitleCrystal structure of the DEADc domain of human translation initiation factor 4A-2
ComponentsHuman initiation factor 4A-II
KeywordsHYDROLASE / translation initiation / DEAD box / structural genomics / helicase / ATP-binding / Host-virus interaction / Initiation factor / Nucleotide-binding / Protein biosynthesis / RNA-binding / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of RNA-dependent RNA polymerase activity / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulation of translational initiation / Ribosomal scanning and start codon recognition / Translation initiation complex formation ...negative regulation of RNA-dependent RNA polymerase activity / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulation of translational initiation / 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 / translation initiation factor activity / cellular response to leukemia inhibitory factor / translational initiation / helicase activity / ISG15 antiviral mechanism / RNA helicase activity / RNA helicase / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / ATP binding / cytosol
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 domain / DEAD/DEAH box helicase / 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 domain / DEAD/DEAH box helicase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic initiation factor 4A-II
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsDimov, S. / Hong, B. / Tempel, W. / MacKenzie, F. / Karlberg, T. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bochkarev, A. / Park, H. / 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
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Human initiation factor 4A-II


Theoretical massNumber of molelcules
Total (without water)26,9271
Polymers26,9271
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.093, 80.102, 42.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Human initiation factor 4A-II / ATP-dependent RNA helicase eIF4A-2 / eIF4A-II / eIF-4A-II


Mass: 26927.096 Da / Num. of mol.: 1 / Fragment: DEADc domain: Residues 22-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A2, DDX2B, EIF4F / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q14240, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.85 Å3/Da / Density % sol: 33.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.3
Details: 25% PEG 3350, 0.1M Bis-Tris, 0.2M Ammonium acetate. Chymotrypsin was added to the crystallization sample at a molar ratio of approx. 1:100, pH 7.3, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97242 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 17895 / % possible obs: 100 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.133 / Χ2: 1.659 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.9210.10.65617440.999.9
1.92-1.9910.80.51317450.986100
1.99-2.0811.10.39617641.187100
2.08-2.1911.40.31517481.394100
2.19-2.3311.80.26217721.591100
2.33-2.51120.22217981.725100
2.51-2.7612.10.17717691.819100
2.76-3.16120.12617931.914100
3.16-3.9811.60.08918322.48599.9
3.98-4010.90.06819302.31299.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.3.0037refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
ARP/wARPmodel building
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G9N

2g9n


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.18 / SU B: 2.826 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 883 5 %RANDOM
Rwork0.185 ---
all0.187 ---
obs0.187 17560 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.434 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 0 97 1590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221552
X-RAY DIFFRACTIONr_bond_other_d0.0010.021043
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9732109
X-RAY DIFFRACTIONr_angle_other_deg0.92132568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3245202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24924.35562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40915278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.033158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
X-RAY DIFFRACTIONr_nbd_refined0.1950.2294
X-RAY DIFFRACTIONr_nbd_other0.170.21064
X-RAY DIFFRACTIONr_nbtor_refined0.170.2767
X-RAY DIFFRACTIONr_nbtor_other0.0840.2739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0720.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.28
X-RAY DIFFRACTIONr_mcbond_it2.55121092
X-RAY DIFFRACTIONr_mcbond_other0.6852395
X-RAY DIFFRACTIONr_mcangle_it3.22531588
X-RAY DIFFRACTIONr_scbond_it2.6262623
X-RAY DIFFRACTIONr_scangle_it3.5593516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8980.289690.2061185126599.13
1.898-1.950.246750.1981178126099.444
1.95-2.0060.229660.1891131119999.833
2.006-2.0670.247590.1781125118699.831
2.067-2.1350.245650.1751068113699.736
2.135-2.2090.199550.1751037109699.635
2.209-2.2920.252420.1641028107599.535
2.292-2.3850.234450.178994104299.712
2.385-2.4910.244490.17593098599.391
2.491-2.6110.253540.18588895099.158
2.611-2.7510.271330.19687190899.559
2.751-2.9170.205490.18881286599.538
2.917-3.1160.215330.19477781799.143
3.116-3.3630.232360.19372776599.739
3.363-3.6790.205330.18966670399.431
3.679-4.1060.229230.17362264699.845
4.106-4.7260.17300.14555258399.828
4.726-5.7530.225260.20246449199.796
5.753-7.990.253280.234375403100
7.99-300.179130.22224726199.617

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