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- PDB-5abv: Complex of D. melanogaster eIF4E with the 4E-binding protein Mextli -

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Basic information

Entry
Database: PDB / ID: 5abv
TitleComplex of D. melanogaster eIF4E with the 4E-binding protein Mextli
Components
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
  • GH11071P
KeywordsTRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E BINDING PROTEIN
Function / homology
Function and homology information


regulation of formation of translation initiation ternary complex / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / Translation initiation complex formation ...regulation of formation of translation initiation ternary complex / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / Translation initiation complex formation / Ribosomal scanning and start codon recognition / female germ-line stem cell population maintenance / muscle cell postsynaptic specialization / RNA cap binding complex / RNA metabolic process / neuronal ribonucleoprotein granule / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translation initiation factor activity / positive regulation of translation / neuromuscular junction / translational initiation / P-body / cytoplasmic ribonucleoprotein granule / regulation of translation / nuclear body / translation / RNA binding / cytoplasm / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 4E-binding protein Mextli / 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 / KH domain / K Homology domain, type 1 ...Eukaryotic translation initiation factor 4E-binding protein Mextli / 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 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E1 / Eukaryotic translation initiation factor 4E-binding protein Mextli
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsPeter, D. / Weichenrieder, O.
CitationJournal: Genes Dev. / Year: 2015
Title: Mextli Proteins Use Both Canonical Bipartite and Novel Tripartite Binding Modes to Form Eif4E Complexes that Display Differential Sensitivity to 4E-BP Regulation
Authors: Peter, D. / Weber, R. / Koene, C. / Chung, M.-Y. / Ebertsch, L. / Truffault, V. / Weichenrieder, O. / Igreja, C. / Izaurralde, E.
History
DepositionAug 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: GH11071P
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
D: GH11071P
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
F: GH11071P
G: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
H: GH11071P


Theoretical massNumber of molelcules
Total (without water)117,8978
Polymers117,8978
Non-polymers00
Water2,648147
1
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: GH11071P


Theoretical massNumber of molelcules
Total (without water)29,4742
Polymers29,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-16.5 kcal/mol
Surface area12460 Å2
MethodPISA
2
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
D: GH11071P


Theoretical massNumber of molelcules
Total (without water)29,4742
Polymers29,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-17.9 kcal/mol
Surface area12060 Å2
MethodPISA
3
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
F: GH11071P


Theoretical massNumber of molelcules
Total (without water)29,4742
Polymers29,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-17.3 kcal/mol
Surface area12090 Å2
MethodPISA
4
G: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
H: GH11071P


Theoretical massNumber of molelcules
Total (without water)29,4742
Polymers29,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-16.9 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.900, 82.020, 84.730
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / EIF-4E / EIF4E / EIF-4F 25 KDA SUBUNIT / MRNA CAP-BINDING PROTEIN


Mass: 21249.037 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 69-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P48598
#2: Protein
GH11071P / 4E-BINDING PROTEIN MEXTLI


Mass: 8225.225 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 577-640
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9VR35
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNUMBERING OF CHAIN A, C, E, G CORRESPONDS TO UNP P48598-2. COMPARED TO UNP P48598, SEQUENCE NUMBERS ...NUMBERING OF CHAIN A, C, E, G CORRESPONDS TO UNP P48598-2. COMPARED TO UNP P48598, SEQUENCE NUMBERS ARE SHIFTED BY - 11 RESIDUES. THE FIRST FOUR RESIDUES OF CHAINS A, C, E, G REMAIN FROM THE EXPRESSION TAG. THE FIRST SIX RESIDUES OF CHAINS B, D, F, H REMAIN FROM THE EXPRESSION TAG.

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6 / Details: 0.1M BISTRIS PH=6.0, 23% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.13→44 Å / Num. obs: 50587 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 45.69 Å2 / Rsym value: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.44 / % possible all: 90.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UE8 CHAIN A

4ue8


Resolution: 2.13→43.96 Å / Cor.coef. Fo:Fc: 0.9479 / Cor.coef. Fo:Fc free: 0.9228 / SU R Cruickshank DPI: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.258 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.198
Details: REFINEMENT WAS DONE WITH ONE TLS GROUP PER CHAIN AND BUSTER AUTO NCS. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 238 TO 240. CHAIN B, RESIDUES 639, 640. CHAIN C, RESIDUES ...Details: REFINEMENT WAS DONE WITH ONE TLS GROUP PER CHAIN AND BUSTER AUTO NCS. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 238 TO 240. CHAIN B, RESIDUES 639, 640. CHAIN C, RESIDUES 151,152,189,190,238 TO 241. CHAIN D, RESIDUES 638 TO 640. CHAIN E, RESIDUES 238 TO 240. CHAIN F, RESIDUES 636 TO 640. CHAIN G, RESIDUES 220, 221, 237 TO 240. CHAIN H, RESIDUES 637 TO 640. IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 2443 4.92 %RANDOM
Rwork0.1916 ---
obs0.1937 49675 98.22 %-
Displacement parametersBiso mean: 65.39 Å2
Baniso -1Baniso -2Baniso -3
1--5.2464 Å20 Å20.7801 Å2
2---7.9037 Å20 Å2
3---13.1502 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.13→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7790 0 0 147 7937
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017971HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0510784HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2814SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes234HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1099HARMONIC5
X-RAY DIFFRACTIONt_it7971HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion18.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1020SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8846SEMIHARMONIC4
LS refinement shellResolution: 2.13→2.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3057 139 4.11 %
Rwork0.2295 3239 -
all0.2325 3378 -
obs--90.47 %
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)
11.41910.4891-0.4192.3083-1.17335.9698-0.080.2032-0.1154-0.2824-0.261-0.33830.4410.55160.341-0.2520.08420.03510.06130.0553-0.1464-20.129143.106854.1843
25.25921.24641.11563.90591.24723.13980.1148-0.3905-0.06910.3954-0.1428-0.13740.5388-0.06940.028-0.086-0.0185-0.0288-0.00330.0573-0.1375-23.363639.412672.099
30.74450.29840.24531.3486-1.142510.47330.1090.0341-0.0291-0.1180.10960.04141.0892-0.4675-0.2186-0.2174-0.0666-0.08630.04440.0216-0.257-20.07041.824150.8525
42.93141.8118-0.51114.9833-2.28668.03370.1524-0.23040.148-0.08320.0196-0.01621.0892-0.8427-0.172-0.0573-0.1289-0.09540.04940.0493-0.3169-22.708-1.630468.7234
51.19610.281-0.09741.35940.92279.68360.07940.07530.06-0.11650.1169-0.0058-1.08790.4362-0.1962-0.2052-0.07250.09380.0649-0.0441-0.2891-13.098417.47568.2973
63.57952.32581.02744.47331.65857.26910.069-0.1905-0.17790.010.1053-0.0188-1.08790.83-0.1743-0.0486-0.15360.09630.1119-0.078-0.3112-9.867620.52226.4271
71.20630.42490.65522.17961.25225.8282-0.07790.21490.1265-0.3138-0.26380.3415-0.469-0.50020.3417-0.23870.0857-0.02910.0577-0.0333-0.1266-12.8381-24.227411.9224
85.42791.9067-0.71544.4819-1.80563.76240.0394-0.30380.12790.4327-0.07340.1437-0.53580.0490.034-0.1001-0.02130.0205-0.0286-0.0609-0.1332-9.426-21.01729.6204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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