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- PDB-6fc2: Crystal structure of the eIF4E-Eap1p complex from Saccharomyces c... -

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Basic information

Entry
Database: PDB / ID: 6fc2
TitleCrystal structure of the eIF4E-Eap1p complex from Saccharomyces cerevisiae
Components
  • Eukaryotic translation initiation factor 4E
  • Protein EAP1
KeywordsTRANSLATION / Gene expression Translation Translational control 4E-binding proteins
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 / eukaryotic initiation factor 4E binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...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 / eukaryotic initiation factor 4E binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of translational initiation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mRNA catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor activity / translational initiation / cytoplasmic stress granule / regulation of cell cycle / negative regulation of translation / ribosome / mRNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
eIF4E-associated protein / eIF4E-associated protein / 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 / Protein EAP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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.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_label_seq_id

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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: Protein EAP1
C: Eukaryotic translation initiation factor 4E
D: Protein EAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8345
Polymers56,7944
Non-polymers401
Water3,927218
1
A: Eukaryotic translation initiation factor 4E
B: Protein EAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4373
Polymers28,3972
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-30 kcal/mol
Surface area12210 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E
D: Protein EAP1


Theoretical massNumber of molelcules
Total (without water)28,3972
Polymers28,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-25 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.574, 95.116, 56.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CDC33, TIF45, YOL139C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07260
#2: Protein Protein EAP1 / eIF4E-associated protein 1


Mass: 7590.755 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: EAP1, YKL204W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36041
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes-NaOH (pH 7.5) 30% (w/v) Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.92→48.263 Å / Num. obs: 36515 / % possible obs: 100 % / Redundancy: 13.2 % / Rsym value: 0.105 / Net I/σ(I): 17.5
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 30566 / Num. unique obs: 2408 / CC1/2: 0.542 / Rsym value: 1.711 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FBZ, chain A

6fbz


Resolution: 1.92→48.263 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.91
RfactorNum. reflection% reflection
Rfree0.2065 1786 4.9 %
Rwork0.1735 --
obs0.175 36466 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.92→48.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3876 0 1 218 4095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014004
X-RAY DIFFRACTIONf_angle_d0.7475432
X-RAY DIFFRACTIONf_dihedral_angle_d15.972383
X-RAY DIFFRACTIONf_chiral_restr0.044576
X-RAY DIFFRACTIONf_plane_restr0.005695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.97190.29881420.27172618X-RAY DIFFRACTION100
1.9719-2.02990.28881250.24072627X-RAY DIFFRACTION100
2.0299-2.09550.26051360.22322619X-RAY DIFFRACTION100
2.0955-2.17040.2491410.20652643X-RAY DIFFRACTION100
2.1704-2.25730.22551090.19082663X-RAY DIFFRACTION100
2.2573-2.360.22411510.18242619X-RAY DIFFRACTION100
2.36-2.48440.20481490.17972638X-RAY DIFFRACTION100
2.4844-2.64010.21141490.17422637X-RAY DIFFRACTION100
2.6401-2.84390.22691420.17532649X-RAY DIFFRACTION100
2.8439-3.130.24131590.1712663X-RAY DIFFRACTION100
3.13-3.58280.20581410.15832687X-RAY DIFFRACTION100
3.5828-4.51340.13881220.14162736X-RAY DIFFRACTION100
4.5134-48.27830.19681200.17592881X-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)
12.36510.40270.68643.6307-0.26791.74060.0366-0.1308-0.26130.07650.05080.02280.12090.0424-0.09650.18190.007-0.02030.1832-0.00680.1971114.4145107.61581.1921
22.73923.9168-4.46357.2113-4.99598.5814-0.1530.131-0.5806-0.29620.0173-0.9070.10740.86440.23780.245-0.01050.03040.3684-0.04380.3577121.298108.760778.5551
32.7139-0.1322-0.00712.6369-0.70592.71350.0560.0265-0.1822-0.13370.10790.12080.0105-0.193-0.16790.2588-0.0079-0.01560.2328-0.00620.2502109.5633107.61576.9484
45.409-1.9057-1.12998.424.14398.2372-0.0447-0.1368-0.2305-0.14630.3479-0.87160.30730.7865-0.22930.30990.0361-0.02630.32530.00290.5273124.990695.259178.0288
54.0901-4.4384-2.349.5758-0.25444.47310.37720.57680.528-1.4328-0.1281-0.4248-0.1283-0.9583-0.21090.546-0.0523-0.06120.4232-0.01450.4258110.224298.817462.1044
62.36630.1881-0.10342.6897-0.18431.85640.04670.2014-0.6247-0.19080.05230.09370.3188-0.1417-0.07590.2864-0.0366-0.03810.2381-0.04050.3641110.655393.655671.9885
72.4609-2.1749-2.47955.222-0.28514.35330.04240.775-0.2414-0.7295-0.0435-0.06970.5853-0.2189-0.0860.5404-0.0517-0.00270.4176-0.15250.4452114.226889.765861.8857
83.5027-0.33481.5034.43131.65424.11080.2013-0.1589-0.7930.0566-0.01380.88120.6122-0.0855-0.09630.3684-0.09290.00010.36730.09090.576399.511691.423581.6585
92.96880.4464-0.90893.0775-0.71056.0811-0.0866-0.1528-0.0193-0.0004-0.06380.1973-0.2494-0.3079-0.04960.26430.0536-0.00530.24870.00150.3047107.0102115.731282.6148
104.63242.57841.34894.2295-1.07433.5377-0.29050.6234-0.1092-0.72440.2266-0.04940.1628-0.178-0.0150.2520.00250.03860.3979-0.02190.207187.8269118.091956.7703
112.42521.4384-1.32731.68650.18511.8602-0.25680.46111.2088-0.54670.1507-1.1101-2.11060.4012-0.13130.7347-0.0788-0.04530.39160.19690.8956104.7251138.540464.5978
122.14930.4287-1.07056.8683-2.12819.8102-0.05320.130.346-0.5568-0.0518-0.3419-1.03550.60650.12330.24250.0076-0.00860.4170.05790.326595.7803130.04458.4507
130.0857-0.0482-0.06810.11160.07690.07060.07670.4281-0.5171-0.211-0.22790.00050.46050.1941-0.00030.35190.00830.01290.44820.00390.275692.5839111.957258.3415
145.1038-0.6733-0.1153.03740.06442.01580.08160.73160.63-0.1231-0.1624-0.2152-0.12610.10790.08030.2637-0.00290.02260.27640.07270.25589.9285128.522163.1866
153.6799-4.68783.42877.3186-2.45646.3645-0.1672-0.5810.48550.8826-0.0971-1.0929-0.05140.49690.40550.3839-0.0404-0.07340.46450.07550.443788.3562125.171178.5332
163.7379-0.8236-1.43591.46530.26372.1439-0.07880.02370.10840.11540.04750.03420.0283-0.11840.03310.2757-0.0093-0.02320.25420.01760.218781.6757122.211471.2905
176.65971.25160.41042.54991.84297.02150.0373-0.39431.0161-0.11550.0141-0.3457-0.72340.264-0.0450.38820.04110.03670.3203-0.02980.473278.8199135.025576.4468
184.19890.8383-2.88574.07422.8484.9884-0.0962-0.4549-0.87481.09730.3295-0.47641.47580.0056-0.35780.5088-0.0269-0.06820.38940.04360.488380.7052107.420375.1836
192.3438-1.02283.5431.6103-2.11815.63710.08960.0233-0.6805-0.17940.59990.59490.7501-0.9899-0.70250.3717-0.1164-0.06760.59590.0720.410573.0892111.379760.9082
205.3621-4.4665-1.79394.71760.85054.3695-0.2212-0.5795-1.22290.8788-0.7149-0.47690.35760.30750.54450.4859-0.0310.00540.21120.09910.522585.3162105.701866.0386
213.8572-2.81493.00082.6921-1.04425.0502-0.11980.8198-0.3985-0.84760.9586-0.6321-0.67371.1546-0.73880.8626-0.15770.14080.7211-0.06750.632898.1348103.059856.417
224.42413.06123.23965.45452.57212.40530.17871.6055-0.3127-2.18020.4171-0.5913-0.6802-0.5832-0.43490.644-0.0180.13390.68930.03180.408998.5707112.199549.4489
236.35981.33373.12399.38955.21733.97830.22680.2155-0.6563-0.27360.4297-1.7699-0.06491.1436-0.7090.3585-0.06030.0090.48080.06040.6445104.9819122.528759.0546
244.1119-2.93064.74169.4745-1.05156.2016-0.0211-0.4761.28391.80730.3363-1.1711-0.04751.2835-0.22820.5570.1334-0.03360.86870.05590.606109.3133126.596169.2456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 125 )
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 185 )
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 213 )
8X-RAY DIFFRACTION8chain 'B' and (resid 91 through 117 )
9X-RAY DIFFRACTION9chain 'B' and (resid 118 through 150 )
10X-RAY DIFFRACTION10chain 'C' and (resid 35 through 48 )
11X-RAY DIFFRACTION11chain 'C' and (resid 49 through 57 )
12X-RAY DIFFRACTION12chain 'C' and (resid 58 through 68 )
13X-RAY DIFFRACTION13chain 'C' and (resid 69 through 80 )
14X-RAY DIFFRACTION14chain 'C' and (resid 81 through 112 )
15X-RAY DIFFRACTION15chain 'C' and (resid 113 through 125 )
16X-RAY DIFFRACTION16chain 'C' and (resid 126 through 193 )
17X-RAY DIFFRACTION17chain 'C' and (resid 194 through 213 )
18X-RAY DIFFRACTION18chain 'D' and (resid 91 through 96 )
19X-RAY DIFFRACTION19chain 'D' and (resid 97 through 110 )
20X-RAY DIFFRACTION20chain 'D' and (resid 111 through 117 )
21X-RAY DIFFRACTION21chain 'D' and (resid 118 through 129 )
22X-RAY DIFFRACTION22chain 'D' and (resid 130 through 137 )
23X-RAY DIFFRACTION23chain 'D' and (resid 138 through 145 )
24X-RAY DIFFRACTION24chain 'D' and (resid 146 through 150 )

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