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- PDB-3u7x: Crystal structure of the human eIF4E-4EBP1 peptide complex without cap -

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Basic information

Entry
Database: PDB / ID: 3u7x
TitleCrystal structure of the human eIF4E-4EBP1 peptide complex without cap
Components
  • Eukaryotic translation initiation factor 4E-binding protein 1
  • Eukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION / eIF4E / 4EBP1 / mRNA export / structural genomics consortium / SGC
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 4G binding / eukaryotic initiation factor 4E binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / : ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / : / Deadenylation of mRNA / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / stem cell population maintenance / TOR signaling / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / behavioral fear response / mRNA export from nucleus / translation initiation factor binding / translation repressor activity / negative regulation of translational initiation / translational initiation / translation initiation factor activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / P-body / G1/S transition of mitotic cell cycle / neuron differentiation / cytoplasmic ribonucleoprotein granule / ISG15 antiviral mechanism / cytoplasmic stress granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear speck / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / 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
Eukaryotic translation initiation factor 4E / Eukaryotic translation initiation factor 4E-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSiddiqui, N. / Tempel, W. / Nedyalkova, L. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Borden, K.L.B. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Insights into the Allosteric Effects of 4EBP1 on the Eukaryotic Translation Initiation Factor eIF4E.
Authors: Siddiqui, N. / Tempel, W. / Nedyalkova, L. / Volpon, L. / Wernimont, A.K. / Osborne, M.J. / Park, H.W. / Borden, K.L.
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionNov 2, 2011ID: 3SMU
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4E
C: Eukaryotic translation initiation factor 4E-binding protein 1
D: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,36028
Polymers54,9764
Non-polymers38424
Water2,216123
1
A: Eukaryotic translation initiation factor 4E
C: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,58412
Polymers27,4882
Non-polymers9610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-22 kcal/mol
Surface area10850 Å2
MethodPISA
2
B: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,77616
Polymers27,4882
Non-polymers28814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-37 kcal/mol
Surface area10720 Å2
MethodPISA
3
B: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules

A: Eukaryotic translation initiation factor 4E
C: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,36028
Polymers54,9764
Non-polymers38424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area4130 Å2
ΔGint-65 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.500, 38.263, 93.533
Angle α, β, γ (deg.)90.000, 97.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRARGARGDD50 - 634 - 17
21THRTHRARGARGCC50 - 634 - 17
12ASNASNTRPTRPAA50 - 5650 - 56
22ASNASNTRPTRPBB50 - 5650 - 56

NCS ensembles :
ID
1
2

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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: 25130.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06730
#2: Protein/peptide Eukaryotic translation initiation factor 4E-binding protein 1 / 4E-BP1 / eIF4E-binding protein 1 / Phosphorylated heat- and acid-stable protein regulated by ...4E-BP1 / eIF4E-binding protein 1 / Phosphorylated heat- and acid-stable protein regulated by insulin 1 / PHAS-I


Mass: 2357.755 Da / Num. of mol.: 2 / Fragment: UNP residues 46-66 / Source method: obtained synthetically
Details: Fmoc solid-phase peptide synthesis (Sheldon Biotechnology Center)
Source: (synth.) Homo sapiens (human) / References: UniProt: Q13541
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 20 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium ...Details: 1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium HEPES), vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 35859 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.089 / Χ2: 1.282 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.143.40.6417281.036196.9
2.14-2.183.50.57117031.056198.7
2.18-2.223.60.48118001.155199.4
2.22-2.263.60.48617662.18199.4
2.26-2.313.70.45717691.305199.7
2.31-2.373.70.37317841.155199.9
2.37-2.423.70.31817861.142199.9
2.42-2.493.70.30717681.1551100
2.49-2.563.70.26818181.1831100
2.56-2.653.70.22317481.1211100
2.65-2.743.70.18818011.154199.8
2.74-2.853.70.14517601.1421100
2.85-2.983.70.11318201.1321100
2.98-3.143.70.08318101.1681100
3.14-3.333.70.06617871.1981100
3.33-3.593.70.05418281.3431100
3.59-3.953.70.05417911.727199.7
3.95-4.523.60.04718271.8321100
4.52-5.73.50.03718361.2991100
5.7-503.50.03119291.139199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IPB

1ipb


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.957 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. AMINO ACID RESIDUES 51 THROUGH 58 ARE POORLY DEFINED BY ELECTRON DENSITY. FO-FC DENSITY SUGGESTS AN ALTERNATE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. AMINO ACID RESIDUES 51 THROUGH 58 ARE POORLY DEFINED BY ELECTRON DENSITY. FO-FC DENSITY SUGGESTS AN ALTERNATE CONFORMATION OF THIS REGION FOR CHAIN A. AUTOBUSTER, PHENIX, COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT OF THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1503 4.211 %THIN SHELLS (SFTOOLS)
Rwork0.1982 ---
obs0.199 35692 98.947 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso max: 114.74 Å2 / Biso mean: 41.169 Å2 / Biso min: 27.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.746 Å20 Å22.148 Å2
2---0.441 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 40 123 3368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213391
X-RAY DIFFRACTIONr_bond_other_d0.0010.022319
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9364615
X-RAY DIFFRACTIONr_angle_other_deg0.89435588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03322.848165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49915562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7831531
X-RAY DIFFRACTIONr_chiral_restr0.080.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023810
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02763
X-RAY DIFFRACTIONr_mcbond_it0.6881.52043
X-RAY DIFFRACTIONr_mcbond_other0.1471.5831
X-RAY DIFFRACTIONr_mcangle_it1.25723278
X-RAY DIFFRACTIONr_scbond_it1.90231348
X-RAY DIFFRACTIONr_scangle_it3.0244.51326
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1D81MEDIUM POSITIONAL0.290.5
1D89LOOSE POSITIONAL0.225
1D81MEDIUM THERMAL0.192
1D89LOOSE THERMAL0.2410
2A42MEDIUM POSITIONAL0.120.5
2A15LOOSE POSITIONAL0.215
2A42MEDIUM THERMAL0.162
2A15LOOSE THERMAL0.3310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15400.2742382262490.777
2.154-2.2130.2941690.2412365255199.334
2.213-2.2770.2971520.2362348251599.404
2.277-2.34600.212410241799.71
2.346-2.4230.2511390.1972200234399.829
2.423-2.5070.2341400.1932108225799.601
2.507-2.6010.2161140.1952088220799.773
2.601-2.7070.2331010.2062013212899.342
2.707-2.82600.1932016202499.605
2.826-2.9630.247960.1851884198699.698
2.963-3.1210.224870.1841739183399.618
3.121-3.3080.198740.1931661174799.313
3.308-3.5340.176650.1931603167199.82
3.534-3.8120.198830.1851480156999.618
3.812-4.1690.202880.1781324142399.227
4.169-4.650.177490.1661254130899.618
4.65-5.3480.199570.1761102116299.742
5.348-6.4990.26400.229964100799.702
6.499-8.9830.32280.22375778899.619
8.983-300.257210.232491512100
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)
12.06860.2282-1.48392.1662-0.65025.06280.0068-0.0791-0.0832-0.02120.0138-0.09170.14950.0776-0.02060.0681-0.0252-0.01530.0112-0.00120.013938.1223-7.282918.1657
24.5964-1.0078-0.47282.35140.45521.4817-0.03940.1048-0.0225-0.1162-0.04310.0613-0.0172-0.11110.08250.0204-0.0012-0.02650.0155-0.02430.059661.30980.482347.2028
34.73945.36560.811914.29842.96017.66770.11710.7830.173-1.0067-0.29050.25830.0499-0.33010.17330.24010.0435-0.04780.45190.07960.247828.4804-2.19644.6319
48.73455.28020.446817.19653.32788.721-0.0609-0.6796-0.03420.3767-0.2368-0.7951-0.10190.86580.29770.16140.0999-0.05350.37810.06350.195472.6173-4.123559.3549
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 217
2X-RAY DIFFRACTION2B31 - 217
3X-RAY DIFFRACTION3C50 - 63
4X-RAY DIFFRACTION4D50 - 63

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