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- PDB-4axg: Structure of eIF4E-Cup complex -

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Basic information

Entry
Database: PDB / ID: 4axg
TitleStructure of eIF4E-Cup complex
Components
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4EEIF4E
  • PROTEIN CUP
KeywordsTRANSLATION / 4E-BP / MRNA LOCALIZATION
Function / homology
Function and homology information


oocyte growth in germarium-derived egg chamber / negative regulation of eukaryotic translation initiation factor 4F complex assembly / follicle cell of egg chamber migration / negative regulation of oskar mRNA translation / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / ISG15 antiviral mechanism / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript ...oocyte growth in germarium-derived egg chamber / negative regulation of eukaryotic translation initiation factor 4F complex assembly / follicle cell of egg chamber migration / negative regulation of oskar mRNA translation / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / ISG15 antiviral mechanism / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / mTORC1-mediated signalling / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / muscle cell postsynaptic specialization / regulation of pole plasm oskar mRNA localization / trans-synaptic signaling / regulation of synaptic assembly at neuromuscular junction / neuronal ribonucleoprotein granule / messenger ribonucleoprotein complex / RNA metabolic process / meiotic chromosome segregation / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / intracellular mRNA localization / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / female meiotic nuclear division / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / dorsal/ventral pattern formation / oogenesis / translation regulator activity / negative regulation of translational initiation / translational initiation / translation initiation factor activity / P-body / neuromuscular junction / terminal bouton / postsynapse / negative regulation of translation / nuclear body / translation / mRNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 4E binding protein / Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E / 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
Eukaryotic translation initiation factor 4E1 / Protein cup
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKinkelin, K. / Veith, K. / Gruenwald, M. / Bono, F.
CitationJournal: RNA / Year: 2012
Title: Crystal Structure of a Minimal Eif4E-Cup Complex Revelas a General Mechanism of Eif4E Regulation in Translational Repression
Authors: Kinkelin, K. / Veith, K. / Gruenwald, M. / Bono, F.
History
DepositionJun 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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

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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: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
C: PROTEIN CUP
D: PROTEIN CUP


Theoretical massNumber of molelcules
Total (without water)85,3344
Polymers85,3344
Non-polymers00
Water25214
1
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
C: PROTEIN CUP


Theoretical massNumber of molelcules
Total (without water)42,6672
Polymers42,6672
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-14.3 kcal/mol
Surface area11620 Å2
MethodPISA
2
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
D: PROTEIN CUP


Theoretical massNumber of molelcules
Total (without water)42,6672
Polymers42,6672
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-8 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.580, 142.580, 108.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B

NCS oper: (Code: given
Matrix: (-0.4093, -0.90467, 0.11854), (0.63893, -0.19144, 0.74506), (-0.65134, 0.38069, 0.65638)
Vector: 14.13856, -67.63185, 12.28072)

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Components

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


Mass: 27861.111 Da / Num. of mol.: 2 / Fragment: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P48598
#2: Protein PROTEIN CUP / OSKAR RIBONUCLEOPROTEIN COMPLEX 147 KDA SUBUNIT


Mass: 14805.982 Da / Num. of mol.: 2 / Fragment: RESIDUE 296-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9VMA3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.17 Å3/Da / Density % sol: 61.2 % / Description: NONE
Crystal growDetails: 20% PEG3350, 200 MM CALCIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0718
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 2.8→81.31 Å / Num. obs: 16494 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Biso Wilson estimate: 67.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.23
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 13.62 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 2.79 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U7X

3u7x


Resolution: 2.8→81.314 Å / SU ML: 0.46 / σ(F): 2 / Phase error: 24.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2442 825 5 %
Rwork0.2282 --
obs0.2291 16464 99.95 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.731 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 85.45 Å2
Baniso -1Baniso -2Baniso -3
1-6.1776 Å20 Å20 Å2
2--6.1776 Å20 Å2
3----12.3553 Å2
Refinement stepCycle: LAST / Resolution: 2.8→81.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 0 14 3047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033094
X-RAY DIFFRACTIONf_angle_d0.6534213
X-RAY DIFFRACTIONf_dihedral_angle_d13.3141047
X-RAY DIFFRACTIONf_chiral_restr0.047477
X-RAY DIFFRACTIONf_plane_restr0.002538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1440X-RAY DIFFRACTIONPOSITIONAL
12B1440X-RAY DIFFRACTIONPOSITIONAL0.472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.97560.36111340.31442551X-RAY DIFFRACTION100
2.9756-3.20530.25691340.26282537X-RAY DIFFRACTION100
3.2053-3.52790.27241350.22982554X-RAY DIFFRACTION100
3.5279-4.03840.26171360.21082596X-RAY DIFFRACTION100
4.0384-5.08780.2351390.18972622X-RAY DIFFRACTION100
5.0878-81.34790.21181470.24482779X-RAY DIFFRACTION100
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)
11.82341.16290.69412.25330.35643.8905-0.04260.32010.1848-0.1307-0.00680.089-0.52570.17430.07630.5282-0.1337-0.08870.30750.04250.383547.0754-34.3053-3.3237
21.81120.650.54171.0427-0.50633.7444-0.30260.3635-0.0497-0.14070.2679-0.2616-0.1177-0.38970.02190.6726-0.3448-0.21150.87430.07970.593135.6095-48.0844-23.4612
31.72730.60870.85691.69060.1513.5505-0.3864-0.0740.1361-0.32030.09040.1275-0.3565-0.1264-0.0490.363-0.0107-0.05960.37860.03760.472939.9452-40.5345-5.0435
45.7524-3.53291.4543.8329-2.0093.05350.54131.8426-0.0834-1.8768-0.6343-0.1083-0.5190.2886-0.13020.8466-0.1935-0.08760.7268-0.0190.41652.4546-44.1928-18.5359
52.5069-1.8127-0.28331.50080.56475.03320.22330.5408-0.6317-0.1990.15880.46431.4394-0.11090.26870.4979-0.1062-0.07530.36890.01670.509345.8535-58.2774-5.3899
61.9064-0.3693-0.15623.0913-0.45043.66060.00260.2361-0.309-0.22630.0347-0.00680.01970.4624-0.01670.2021-0.0994-0.05680.2667-0.01310.322351.4735-50.5023-3.8908
73.12040.0372-2.5822.7093-0.49376.20390.06941.3759-0.7789-0.82550.166-0.06331.4377-0.88790.08190.5576-0.0606-0.11030.4316-0.17250.510751.8512-59.2908-7.4025
85.00190.76851.48330.642-0.76632.3342-0.50321.143-1.4479-0.26070.42140.68211.5079-0.1547-0.84450.9564-0.0169-0.0840.5765-0.36870.994753.9483-62.6161-12.8067
90.13040.25-0.3230.9743-1.08852.06730.3461-0.1254-0.0406-0.5471-0.6404-0.4643-0.28411.02920.15620.5491-0.05880.10910.6880.08280.433461.0998-35.22541.2133
101.4585-0.83380.24593.4441-0.5934.582-0.7839-1.1017-0.02190.65810.61720.5947-0.0684-0.30190.0070.3728-0.03410.0240.43480.0040.415145.2761-38.540810.532
113.35821.66071.09872.1346-0.89061.9260.09340.28290.5427-0.0853-1.04040.1903-1.071-0.4318-0.1940.92120.4842-0.3230.90240.05980.946631.0659-32.7354-8.6174
124.0535-3.63423.30053.5833-3.07653.00040.2979-0.01751.03150.227-0.72360.0266-0.0778-0.6083-0.24081.0110.0362-0.21140.6775-0.17990.87730.0853-38.9254-4.6485
132.36941.29650.55822.1062-0.66635.37280.28260.30380.6642-0.17810.63181.2547-0.1119-2.06370.81530.2789-0.5939-0.62991.1344-0.00260.197832.6069-37.7694-33.8076
141.7485-0.74311.0851.60720.21672.51060.01211.46510.3141-1.37390.12280.17650.2909-0.61140.12190.7173-0.3669-0.14061.02720.2520.361539.2266-32.8357-41.7325
152.049-1.72780.91145.692-4.54986.1631-0.24831.36330.8834-0.95630.480.8566-0.4318-1.7928-0.54070.9715-0.2684-0.31711.34950.26950.717833.7934-28.8371-43.8618
162.96510.31271.07663.8192-0.78434.98930.01341.0370.3744-0.7610.17190.3947-0.6814-0.86520.05150.8522-0.2614-0.17031.11690.33240.846539.8681-28.027-47.034
174.2425-2.41711.34184.51430.77681.17050.45830.93580.5045-1.17890.4278-0.50860.5294-0.46410.55921.369-0.59340.00621.40630.25570.753146.0724-28.7737-49.0696
182.79030.15670.53632.11130.65161.70390.05691.46710.9372-1.45520.79240.29310.38570.31210.08491.8551-0.24110.23811.35240.2990.785946.2153-28.8172-55.416
199.74350.8013-0.39947.3328-0.04941.8124-0.74470.21750.9642-0.55420.18511.4482-1.71810.07450.00830.88950.1096-0.06630.8461-0.11381.073429.8954-22.8824-27.2943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 66:81)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 82:92)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 93:128)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 129:143)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 144:154)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 155:217)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 218:235)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 236:248)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 318:328)
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 329:339)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 362:370)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 371:376)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 69:128)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 129:170)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 171:187)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 188:218)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 219:234)
18X-RAY DIFFRACTION18CHAIN B AND (RESSEQ 235:248)
19X-RAY DIFFRACTION19CHAIN D AND (RESSEQ 325:339)

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