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- PDB-3m94: Complex crystal structure of Ascaris suum eIF4E-3 with m2,2,7G cap -

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Basic information

Entry
Database: PDB / ID: 3m94
TitleComplex crystal structure of Ascaris suum eIF4E-3 with m2,2,7G cap
Components
  • Eukaryotic translation initiation factor 4E-binding protein 1
  • Translation initiation factor 4E
KeywordsTRANSLATION / eIF4E / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / RNA 7-methylguanosine cap binding / mTORC1-mediated signalling / TOR signaling / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / translation initiation factor activity / positive regulation of mitotic cell cycle ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / RNA 7-methylguanosine cap binding / mTORC1-mediated signalling / TOR signaling / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / translation initiation factor activity / positive regulation of mitotic cell cycle / G1/S transition of mitotic cell cycle / negative regulation of translation / nucleus / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / Chem-M7M / Eukaryotic translation initiation factor 4E-binding protein 1 / eIF-4F 25 kDa subunit
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLiu, W. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural basis for nematode eIF4E binding an m2,2,7G-Cap and its implications for translation initiation.
Authors: Liu, W. / Jankowska-Anyszka, M. / Piecyk, K. / Dickson, L. / Wallace, A. / Niedzwiecka, A. / Stepinski, J. / Stolarski, R. / Darzynkiewicz, E. / Kieft, J. / Zhao, R. / Jones, D.N. / Davis, R.E.
History
DepositionMar 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translation initiation factor 4E
C: Eukaryotic translation initiation factor 4E-binding protein 1
C: ACETYL GROUP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8454
Polymers24,3142
Non-polymers5312
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-9 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.977, 104.977, 46.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Translation initiation factor 4E


Mass: 22169.328 Da / Num. of mol.: 1 / Fragment: UNP residues 49-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm) / Strain: Ascaris suum / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q6PKX2
#2: Protein/peptide Eukaryotic translation initiation factor 4E-binding protein 1 / eIF4E-binding protein 1 / 4E-BP1 / Phosphorylated heat- and acid-stable protein regulated by ...eIF4E-binding protein 1 / 4E-BP1 / Phosphorylated heat- and acid-stable protein regulated by insulin 1 / PHAS-I


Mass: 2144.564 Da / Num. of mol.: 1 / Fragment: UNP residues 51-67 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13541
#3: Chemical ChemComp-M7M / N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)


Mass: 487.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H23N5O11P2
#4: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% MMG PEG 2000, 0.2 M (NH4)2SO4 and 100 mM Na-Critate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2009
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 15993 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.7 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v8W

2v8w


Resolution: 2.05→19.16 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.344 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1632 10.2 %RANDOM
Rwork0.20363 ---
obs0.20766 14361 99.03 %-
all-15993 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.338 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---1.28 Å20 Å2
3---2.56 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 34 39 1631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211632
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9572222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3265190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11923.71878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50615263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2141511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211233
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5321.5959
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9921534
X-RAY DIFFRACTIONr_scbond_it1.6393673
X-RAY DIFFRACTIONr_scangle_it2.4824.5688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 120 -
Rwork0.251 980 -
obs--94.66 %
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)
12.9018-2.6338-2.60452.96780.89217.63130.02590.094-0.07680.1704-0.01320.22050.0575-0.2981-0.01280.2630.00780.0770.15-0.04240.2217-17.344231.141621.2971
25.1529-1.5646-1.68137.05164.43476.0217-0.01090.3446-0.2618-0.05380.17470.00030.20770.0797-0.16380.13040.0115-0.05450.1826-0.06410.1093-8.58520.31857.5596
31.4833-0.1726-2.24945.62274.089.43050.11510.7174-0.1191-0.8883-0.0477-0.0441-0.10210.0724-0.06740.50620.13690.03620.8037-0.17250.311-4.895313.9831-3.0611
41.35710.1489-0.17575.05081.94252.72520.19080.0945-0.0530.1742-0.0391-0.07190.144-0.1481-0.15160.0872-0.0116-0.05480.1296-0.03670.1671-13.963118.647815.9373
53.7236-0.29890.89077.912-0.11154.34360.20140.3023-0.56-0.33590.05530.0550.44950.3715-0.25670.13180.0771-0.06060.1318-0.15240.2107-3.635913.48798.664
67.3454-3.0246-6.8884.57241.29199.46450.17470.8020.3012-0.5204-0.0573-0.23680.1577-0.0573-0.11740.13660.0210.00420.4669-0.0020.1792-3.43526.75414.0054
79.9506-1.88073.76418.7322-4.26737.60930.16040.930.5859-0.27950.0704-0.3266-0.18120.2116-0.23080.1559-0.02460.09380.2741-0.06370.18463.397929.07223.3609
83.47163.2566-1.61649.3254-2.53914.8702-0.1655-0.2881-0.68770.01210.269-0.33460.87640.3866-0.10350.22830.1094-0.10880.2302-0.05810.3886.095911.335418.2919
92.83960.04970.92835.87880.89582.72360.1967-0.0632-0.07310.1914-0.0476-0.23840.03780.271-0.14910.09680.0036-0.03140.1777-0.06890.1726-2.261823.501920.9465
104.15110.34541.25620.094-0.33263.39090.24690.3214-0.25990.0029-0.038-0.02330.13040.6291-0.20890.11670.04810.04460.2573-0.1820.29972.132819.534711.4618
114.95712.50050.82615.6772-0.28343.8077-0.01630.51890.4593-0.2720.1914-0.1913-0.2730.7491-0.17510.0755-0.02370.04190.2969-0.11770.23317.224529.275912.0646
126.13063.9274-0.69788.5059-2.78544.91280.2446-0.4837-0.07820.5476-0.017-0.2004-0.02820.0697-0.22760.09570.0134-0.060.2038-0.11270.156.446925.510123.7943
135.2389-1.31881.42094.579-3.69719.6130.08990.017-0.3307-0.172-0.0466-0.3860.75740.4722-0.04330.1470.0289-0.01790.2235-0.10280.28712.117420.293916.9283
147.5387-3.9791-7.17934.096.1469.83170.1343-0.12510.4991-0.31840.0422-0.2647-0.27260.283-0.17640.2780.11680.16520.43160.11550.621717.833923.546110.397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 40
2X-RAY DIFFRACTION2A41 - 51
3X-RAY DIFFRACTION3A52 - 61
4X-RAY DIFFRACTION4A62 - 84
5X-RAY DIFFRACTION5A85 - 94
6X-RAY DIFFRACTION6A95 - 102
7X-RAY DIFFRACTION7A103 - 112
8X-RAY DIFFRACTION8A113 - 125
9X-RAY DIFFRACTION9A126 - 145
10X-RAY DIFFRACTION10A146 - 161
11X-RAY DIFFRACTION11A162 - 176
12X-RAY DIFFRACTION12A177 - 188
13X-RAY DIFFRACTION13A189 - 200
14X-RAY DIFFRACTION14A201 - 219

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