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

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Basic information

Entry
Database: PDB / ID: 7ppz
TitleCrystal structure of the Burkholderia Lethal Factor 1 (BLF1) C94S inactive mutant in complex with human eIF4A - Crystal form A
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: 2.52 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
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint1 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.980, 50.360, 95.740
Angle α, β, γ (deg.)90.000, 111.920, 90.000
Int Tables number5
Space group name H-MC121

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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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 50 mM magnesium chloride, 10 % (w/v) 2-propanol, 5 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.52→63.07 Å / Num. obs: 20378 / % possible obs: 99.2 % / Redundancy: 3.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.096 / Rrim(I) all: 0.19 / Net I/σ(I): 8.1 / Num. measured all: 76647
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
2.52-2.593.60.725528514570.7030.4410.8521.798.7
11.27-63.073.30.0368032440.9980.0220.04230.294.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TUA and 2ZU6

3tua

2zu6


Resolution: 2.52→63.07 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.865 / SU B: 12.991 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.369 / ESU R Free: 0.349
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2761 1030 5.1 %RANDOM
Rwork0.2016 ---
obs0.2053 19347 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.91 Å2 / Biso mean: 27.593 Å2 / Biso min: 5.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å2-1.42 Å2
2---1.33 Å20 Å2
3---2.9 Å2
Refinement stepCycle: final / Resolution: 2.52→63.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4602 0 0 67 4669
Biso mean---19.43 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0144686
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174217
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.6526340
X-RAY DIFFRACTIONr_angle_other_deg0.9431.6329881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7595575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83822.383256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06215832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7351534
X-RAY DIFFRACTIONr_chiral_restr0.0810.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02852
LS refinement shellResolution: 2.52→2.586 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 80 -
Rwork0.301 1373 -
all-1453 -
obs--98.38 %

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