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- PDB-6fc3: Crystal structure of the eIF4E-p20 complex from Saccharomyces cer... -

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Basic information

Entry
Database: PDB / ID: 6fc3
TitleCrystal structure of the eIF4E-p20 complex from Saccharomyces cerevisiae
Components
  • Cap-associated protein CAF20
  • Eukaryotic translation initiation factor 4E
KeywordsTRANSLATION / Translation Translational control Gene expression 4E-binding protein
Function / homology
Function and homology information


: / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / Deadenylation of mRNA / positive regulation of cytoplasmic mRNA processing body assembly / eukaryotic initiation factor 4E binding / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding ...: / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / Deadenylation of mRNA / positive regulation of cytoplasmic mRNA processing body assembly / eukaryotic initiation factor 4E binding / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translational initiation / translation initiation factor activity / cytoplasmic stress granule / negative regulation of translation / ribosome / regulation of cell cycle / nucleus / cytoplasm
Similarity search - Function
Cap-associated protein Caf20 / Cap associated factor / 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 4E / Cap-associated protein CAF20
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGruener, S. / Valkov, E.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural motifs in eIF4G and 4E-BPs modulate their binding to eIF4E to regulate translation initiation in yeast.
Authors: Gruner, S. / Weber, R. / Peter, D. / Chung, M.Y. / Igreja, C. / Valkov, E. / Izaurralde, E.
History
DepositionDec 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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: Cap-associated protein CAF20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2315
Polymers27,0082
Non-polymers2233
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-63 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.016, 62.755, 44.732
Angle α, β, γ (deg.)90.00, 106.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

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Components

#1: Protein Eukaryotic translation initiation factor 4E / eIF4E / eIF-4F 25 kDa subunit / mRNA cap-binding protein


Mass: 20806.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CDC33, TIF45, YOL139C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07260
#2: Protein Cap-associated protein CAF20 / 20 kDa cap-associated protein / CCR4-associated factor 2 / p20


Mass: 6202.093 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CAF20, CAF2, CAP20, YOR276W, O5453W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12962
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na-acetate (pH 5.0) 13% (w/v) PEG 6000 10 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→48.78 Å / Num. obs: 27294 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rsym value: 0.114 / Net I/σ(I): 8.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1510 / CC1/2: 0.454 / Rsym value: 1.056 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FBZ, chain A

6fbz


Resolution: 1.75→42.78 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 2596 4.98 %
Rwork0.1815 --
obs0.1832 52161 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 8 210 1999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021859
X-RAY DIFFRACTIONf_angle_d1.0312510
X-RAY DIFFRACTIONf_dihedral_angle_d13.3581104
X-RAY DIFFRACTIONf_chiral_restr0.058272
X-RAY DIFFRACTIONf_plane_restr0.007322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78180.29041060.30162648X-RAY DIFFRACTION97
1.7818-1.81610.30741460.29232624X-RAY DIFFRACTION97
1.8161-1.85320.29661500.27822561X-RAY DIFFRACTION97
1.8532-1.89350.31091280.26882589X-RAY DIFFRACTION97
1.8935-1.93750.33251300.26092640X-RAY DIFFRACTION97
1.9375-1.9860.2402980.22812652X-RAY DIFFRACTION99
1.986-2.03970.27261540.21322631X-RAY DIFFRACTION99
2.0397-2.09970.23731320.19872615X-RAY DIFFRACTION97
2.0997-2.16740.22041530.17862591X-RAY DIFFRACTION98
2.1674-2.24490.18991770.17512602X-RAY DIFFRACTION98
2.2449-2.33480.21631270.17362568X-RAY DIFFRACTION96
2.3348-2.4410.22851190.17142613X-RAY DIFFRACTION97
2.441-2.56970.19121450.16882567X-RAY DIFFRACTION97
2.5697-2.73070.24251370.16452641X-RAY DIFFRACTION98
2.7307-2.94150.19451240.15592615X-RAY DIFFRACTION98
2.9415-3.23740.20411610.15872643X-RAY DIFFRACTION99
3.2374-3.70560.17191370.14232634X-RAY DIFFRACTION98
3.7056-4.66780.18611530.13832543X-RAY DIFFRACTION96
4.6678-42.79290.19661190.1862588X-RAY DIFFRACTION96
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)
11.1958-0.23650.31642.205-1.7722.3324-0.0969-0.31540.00730.1690.14560.1794-0.2349-0.3792-0.00310.1390.05020.01310.1862-0.0060.132825.853459.957120.9285
20.28451.1278-0.854.4214-3.54784.5228-0.04290.0369-0.204-0.29450.0717-0.03830.0734-0.3905-0.31750.2567-0.11390.21230.62710.26210.359721.273844.979233.974
31.9036-0.78080.57392.9739-0.92441.5083-0.1534-0.17130.03620.11220.09070.0259-0.1164-0.18760.05860.10620.02130.00950.1165-0.0220.058130.479360.107520.9451
42.1530.7169-0.55642.7490.88532.62230.0013-0.2617-0.10760.05330.0050.5911-0.0941-0.54290.09890.13560.02190.03290.22810.03520.21121.754248.708912.402
53.1297-0.66010.19153.6378-0.81772.70530.03360.0848-0.0295-0.1361-0.01430.09060.0716-0.022-0.04160.08860.00250.0010.0716-0.02420.06733.026753.617511.7015
65.8863-0.2930.63443.65130.44872.9209-0.03940.212-0.0031-0.19880.03220.165-0.043-0.12390.01950.1249-0.0076-0.00120.0704-0.01090.066629.146947.93293.2955
72.12790.1287-1.2471.1996-1.13485.12850.0863-0.4438-0.81330.51370.10020.38790.6251-0.33720.08770.3499-0.0930.03680.24330.09770.373423.21237.33269.377
84.894-1.97215.03493.2297-1.29716.61270.00080.18490.2968-0.0826-0.0854-0.0747-0.13790.25360.05030.1634-0.0055-0.01010.04010.02090.14330.006168.29654.3438
96.96212.2333-1.87351.3451-1.51137.265-0.32280.0280.80260.23450.4557-0.0015-0.86320.3362-0.32330.42110.0435-0.05810.237-0.12410.31233.290170.473524.6044
106.1943-2.77990.55042.87530.28492.9065-0.2176-0.7611-0.43210.23560.4130.15420.0653-0.275-0.15310.1506-0.00040.00240.29190.02560.12137.311349.640434.8672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 119 )
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 161 )
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 198 )
7X-RAY DIFFRACTION7chain 'A' and (resid 199 through 213 )
8X-RAY DIFFRACTION8chain 'B' and (resid -2 through 12 )
9X-RAY DIFFRACTION9chain 'B' and (resid 13 through 23 )
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 45 )

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