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- PDB-5nvn: Crystal structure of the human 4EHP-4E-BP1 complex -

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Basic information

Entry
Database: PDB / ID: 5nvn
TitleCrystal structure of the human 4EHP-4E-BP1 complex
Components
  • Eukaryotic translation initiation factor 4E type 2
  • Eukaryotic translation initiation factor 4E-binding protein 1
KeywordsTRANSLATION / translational regulation / translation initiation / cap-binding protein / eIF4E-binding protein 1
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 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / TOR signaling ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / TOR signaling / mTORC1-mediated signalling / rescue of stalled ribosome / translation initiation factor binding / negative regulation of translational initiation / translation repressor activity / translation initiation factor activity / positive regulation of mitotic cell cycle / P-body / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / negative regulation of translation / ubiquitin protein ligase binding / RNA binding / 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
FORMIC ACID / Eukaryotic translation initiation factor 4E type 2 / Eukaryotic translation initiation factor 4E-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPeter, D. / Sandmeir, F. / Valkov, E.
CitationJournal: Genes Dev. / Year: 2017
Title: GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression.
Authors: Peter, D. / Weber, R. / Sandmeir, F. / Wohlbold, L. / Helms, S. / Bawankar, P. / Valkov, E. / Igreja, C. / Izaurralde, E.
History
DepositionMay 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E type 2
B: Eukaryotic translation initiation factor 4E-binding protein 1
C: Eukaryotic translation initiation factor 4E type 2
D: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,94711
Polymers52,6244
Non-polymers3227
Water3,981221
1
A: Eukaryotic translation initiation factor 4E type 2
B: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3583
Polymers26,3122
Non-polymers461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-14 kcal/mol
Surface area10800 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E type 2
D: Eukaryotic translation initiation factor 4E-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5888
Polymers26,3122
Non-polymers2766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-15 kcal/mol
Surface area11210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.400, 83.390, 70.500
Angle α, β, γ (deg.)90.00, 104.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Eukaryotic translation initiation factor 4E type 2 / eIF4E type 2 / Eukaryotic translation initiation factor 4E homologous protein / Eukaryotic ...eIF4E type 2 / Eukaryotic translation initiation factor 4E homologous protein / Eukaryotic translation initiation factor 4E-like 3 / eIF4E-like protein 4E-LP / mRNA cap-binding protein 4EHP / h4EHP / mRNA cap-binding protein type 3


Mass: 21979.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first six residues of the coordinate sequence belong to the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E2, EIF4EL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: O60573
#2: Protein/peptide Eukaryotic translation initiation factor 4E-binding protein 1 / eIF4E-binding protein 1 / Phosphorylated heat- and acid-stable protein regulated by insulin 1 / PHAS-I


Mass: 4333.087 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first residue of the coordinate sequence belongs to the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4EBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q13541
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.6 1.7 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.9→41.7 Å / Num. obs: 33907 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rsym value: 0.145 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.07 / Num. unique all: 2495 / Rsym value: 1.138 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JGB

2jgb


Resolution: 1.9→41.695 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.85
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1696 5 %Random selection
Rwork0.2264 ---
obs0.2277 33898 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3273 0 21 221 3515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033409
X-RAY DIFFRACTIONf_angle_d0.5294608
X-RAY DIFFRACTIONf_dihedral_angle_d13.0032053
X-RAY DIFFRACTIONf_chiral_restr0.043493
X-RAY DIFFRACTIONf_plane_restr0.003587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8999-1.95580.35531410.30662670X-RAY DIFFRACTION100
1.9558-2.01890.3091410.26772684X-RAY DIFFRACTION100
2.0189-2.0910.28951390.25712643X-RAY DIFFRACTION100
2.091-2.17480.26971400.24592664X-RAY DIFFRACTION100
2.1748-2.27370.30871420.2422693X-RAY DIFFRACTION100
2.2737-2.39360.30541410.23632667X-RAY DIFFRACTION100
2.3936-2.54350.30021410.23712685X-RAY DIFFRACTION100
2.5435-2.73990.25561410.23442684X-RAY DIFFRACTION100
2.7399-3.01560.24731410.23582665X-RAY DIFFRACTION100
3.0156-3.45170.25121420.21892703X-RAY DIFFRACTION100
3.4517-4.34810.2161420.19242707X-RAY DIFFRACTION100
4.3481-41.7050.20011450.21342737X-RAY DIFFRACTION100

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