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- PDB-7pq0: Crystal structure of the Burkholderia Lethal Factor 1 (BLF1) C94S... -

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Basic information

Entry
Database: PDB / ID: 7pq0
TitleCrystal structure of the Burkholderia Lethal Factor 1 (BLF1) C94S inactive mutant in complex with human eIF4A - Crystal form B
Components
  • Burkholderia Lethal Factor 1 (BLF1)
  • Eukaryotic initiation factor 4A-I
KeywordsTOXIN / Glutamine deamidase toxin / cysteine protease / eIf4A complex / CNF1 family
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
Burkholderia lethal factor 1 / Burkholderia lethal factor 1 / 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 ...Burkholderia lethal factor 1 / Burkholderia lethal factor 1 / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Eukaryotic initiation factor 4A-I / Uncharacterized protein
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsMobbs, G.W. / Aziz, A.A. / Dix, S.R. / Blackburn, G.M. / Sedelnikova, S.E. / Minshull, T.C. / Dickman, M.J. / Baker, P.J. / Nathan, S. / Firdaus-Raih, M. / Rice, D.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Royal SocietyIC170306 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M012166/1 United Kingdom
CitationJournal: Commun Biol / Year: 2022
Title: Molecular basis of specificity and deamidation of eIF4A by Burkholderia Lethal Factor 1.
Authors: Mobbs, G.W. / Aziz, A.A. / Dix, S.R. / Blackburn, G.M. / Sedelnikova, S.E. / Minshull, T.C. / Dickman, M.J. / Baker, P.J. / Nathan, S. / Raih, M.F. / Rice, D.W.
History
DepositionSep 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Burkholderia Lethal Factor 1 (BLF1)
B: Eukaryotic initiation factor 4A-I


Theoretical massNumber of molelcules
Total (without water)68,4912
Polymers68,4912
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint4 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.530, 199.530, 51.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Burkholderia Lethal Factor 1 (BLF1)


Mass: 23343.912 Da / Num. of mol.: 1 / Mutation: C94S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain K96243) (bacteria)
Strain: K96243 / Gene: BPSL1549 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q63UP7
#2: Protein Eukaryotic initiation factor 4A-I / eIF-4A-I / eIF4A-I / ATP-dependent RNA helicase eIF4A-1


Mass: 45146.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A1, DDX2A, EIF4A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60842, RNA helicase

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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: 4.38 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 4 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→65.31 Å / Num. obs: 23808 / % possible obs: 99.7 % / Redundancy: 8.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.015 / Rrim(I) all: 0.044 / Net I/σ(I): 34.9 / Num. measured all: 198942
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.088.40.2161430417020.9880.0780.23997.9
13.42-65.316.70.02920063010.9970.0130.03267.998.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHASERphasing
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TUA, 2ZU6, 2G9N

3tua

2zu6

2g9n


Resolution: 3→65.31 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 33.21 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.64 / ESU R Free: 0.321
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 1208 5.1 %RANDOM
Rwork0.186 ---
obs0.1883 22590 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 201.67 Å2 / Biso mean: 95.016 Å2 / Biso min: 66.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----1.71 Å2
Refinement stepCycle: final / Resolution: 3→65.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4716 0 0 0 4716
Num. residues----595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0144804
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174305
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.6536502
X-RAY DIFFRACTIONr_angle_other_deg0.9491.63210096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3665593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50622.368266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03415852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4131536
X-RAY DIFFRACTIONr_chiral_restr0.0730.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 73 -
Rwork0.305 1625 -
all-1698 -
obs--97.75 %
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)
11.2076-0.28020.15031.4060.64160.6699-1.0030.77860.13740.08580.7240.4347-0.12660.28270.2790.8587-0.8185-0.15591.59890.35250.183765.818-55.991-17.607
20.48580.76360.19761.44480.2170.2332-0.07110.3401-0.01640.19540.2050.0652-0.0940.0501-0.13390.8536-0.3433-0.00681.17490.05350.501569.607-65.012.623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 211
2X-RAY DIFFRACTION2B20 - 236
3X-RAY DIFFRACTION2B237 - 240
4X-RAY DIFFRACTION2B241 - 404

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